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Created May 3, 2022 17:31
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docker.log
Sending build context to Docker daemon 4.036MB
Step 1/7 : FROM docker.io/ubuntu:focal-20220426
---> 53df61775e88
Step 2/7 : RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends gcc python3-dev python3-pip nodejs curl libgl1 libegl1
---> Using cache
---> ee5fc7d4cfa6
Step 3/7 : RUN pip3 install cwltool[deps]
---> Using cache
---> 3a9eb28e0313
Step 4/7 : WORKDIR /tmp
---> Using cache
---> db8adaaf0606
Step 5/7 : COPY . .
---> 99e0a57d4182
Step 6/7 : WORKDIR /tmp/simple_use_case/cwl
---> Running in bcbf6ba5ba8e
Removing intermediate container bcbf6ba5ba8e
---> 2a7095fd1c59
Step 7/7 : RUN python3 -m cwltool --debug --beta-conda-dependencies wf_run_use_case.cwl
---> Running in a78ee8837598
INFO /usr/local/lib/python3.8/dist-packages/cwltool/__main__.py 3.1.20220502060230
INFO Resolved 'wf_run_use_case.cwl' to 'file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl'
DEBUG Parsed job order from command line: {
"id": "wf_run_use_case.cwl",
"domain_size": 1.0
}
DEBUG [workflow ] initialized from file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl
INFO [workflow ] start
DEBUG [workflow ] inputs {
"domain_size": 1.0
}
INFO [workflow ] starting step make_mesh
DEBUG [step make_mesh] job input {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#make_mesh/domain_size": 1.0
}
DEBUG [step make_mesh] evaluated job input to {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#make_mesh/domain_size": 1.0
}
INFO [step make_mesh] start
DEBUG [job make_mesh] initializing from file:///tmp/simple_use_case/cwl/make_gmsh_mesh.cwl as part of step make_mesh
DEBUG [job make_mesh] {
"domain_size": 1.0,
"geofile": {
"class": "File",
"location": "file:///tmp/simple_use_case/source/unit_square.geo",
"basename": "unit_square.geo",
"nameroot": "unit_square",
"nameext": ".geo",
"size": 281
}
}
DEBUG [job make_mesh] path mappings is {
"file:///tmp/simple_use_case/source/unit_square.geo": [
"/tmp/simple_use_case/source/unit_square.geo",
"/tmp/pfls8gqy/stgd8228832-2845-49a1-8043-3122d857daaf/unit_square.geo",
"File",
true
]
}
DEBUG [job make_mesh] command line bindings is [
{
"position": [
-1000000,
0
],
"datum": "gmsh"
},
{
"position": [
0,
0
],
"datum": "-setnumber"
},
{
"position": [
0,
1
],
"datum": "domain_size"
},
{
"position": [
0,
2
],
"valueFrom": "$(inputs.domain_size)"
},
{
"position": [
0,
3
],
"datum": "-2"
},
{
"position": [
0,
4
],
"valueFrom": "$(inputs.geofile.path)"
},
{
"position": [
0,
5
],
"datum": "-o"
},
{
"position": [
0,
6
],
"datum": "mesh.msh"
}
]
DEBUG [job make_mesh] initial work dir {}
INFO [job make_mesh] /tmp/porwxmx7$ gmsh \
-setnumber \
domain_size \
1.0 \
-2 \
/tmp/pfls8gqy/stgd8228832-2845-49a1-8043-3122d857daaf/unit_square.geo \
-o \
mesh.msh
Path '/tmp/simple_use_case/cwl/cwltool_deps' does not exist, ignoring
Path '/tmp/simple_use_case/cwl/cwltool_deps' is not directory, ignoring
 % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0  0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
12 67.0M 12 8252k 0 0 8114k 0 0:00:08 0:00:01 0:00:07 8107k
31 67.0M 31 20.9M 0 0 10.3M 0 0:00:06 0:00:02 0:00:04 10.3M
50 67.0M 50 33.7M 0 0 11.1M 0 0:00:05 0:00:03 0:00:02 11.1M
69 67.0M 69 46.6M 0 0 11.6M 0 0:00:05 0:00:04 0:00:01 11.6M
88 67.0M 88 59.4M 0 0 11.8M 0 0:00:05 0:00:05 --:--:-- 11.8M
100 67.0M 100 67.0M 0 0 11.8M 0 0:00:05 0:00:05 --:--:-- 12.7M
PREFIX=/tmp/simple_use_case/cwl/cwltool_deps/_conda
installing: python-3.7.3-h0371630_0 ...
Python 3.7.3
installing: ca-certificates-2019.1.23-0 ...
installing: libgcc-ng-8.2.0-hdf63c60_1 ...
installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: ncurses-6.1-he6710b0_1 ...
installing: openssl-1.1.1b-h7b6447c_1 ...
installing: xz-5.2.4-h14c3975_4 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-h7b6447c_3 ...
installing: libedit-3.1.20181209-hc058e9b_0 ...
installing: readline-7.0-h7b6447c_5 ...
installing: tk-8.6.8-hbc83047_0 ...
installing: sqlite-3.27.2-h7b6447c_0 ...
installing: asn1crypto-0.24.0-py37_0 ...
installing: certifi-2019.3.9-py37_0 ...
installing: chardet-3.0.4-py37_1 ...
installing: idna-2.8-py37_0 ...
installing: pycosat-0.6.3-py37h14c3975_0 ...
installing: pycparser-2.19-py37_0 ...
installing: pysocks-1.6.8-py37_0 ...
installing: ruamel_yaml-0.15.46-py37h14c3975_0 ...
installing: six-1.12.0-py37_0 ...
installing: cffi-1.12.2-py37h2e261b9_1 ...
installing: setuptools-41.0.0-py37_0 ...
installing: cryptography-2.6.1-py37h1ba5d50_0 ...
installing: wheel-0.33.1-py37_0 ...
installing: pip-19.0.3-py37_0 ...
installing: pyopenssl-19.0.0-py37_0 ...
installing: urllib3-1.24.1-py37_0 ...
installing: requests-2.21.0-py37_0 ...
installing: conda-4.6.14-py37_0 ...
installation finished.
Collecting package metadata: ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/simple_use_case/cwl/cwltool_deps/_conda
added / updated specs:
- conda=4.6.14
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
_openmp_mutex-4.5 | 2_gnu 23 KB conda-forge
ca-certificates-2021.10.8 | ha878542_0 139 KB conda-forge
certifi-2021.10.8 | py37h89c1867_2 145 KB conda-forge
cffi-1.15.0 | py37h036bc23_0 225 KB conda-forge
conda-4.6.14 | py37_0 2.1 MB conda-forge
cryptography-36.0.0 | py37h9ce1e76_0 1.5 MB
ld_impl_linux-64-2.36.1 | hea4e1c9_2 667 KB conda-forge
libffi-3.4.2 | h7f98852_5 57 KB conda-forge
libgcc-ng-11.2.0 | h1d223b6_16 902 KB conda-forge
libgomp-11.2.0 | h1d223b6_16 428 KB conda-forge
libnsl-2.0.0 | h7f98852_0 31 KB conda-forge
libstdcxx-ng-11.2.0 | he4da1e4_16 4.2 MB conda-forge
libzlib-1.2.11 | h166bdaf_1014 60 KB conda-forge
ncurses-6.3 | h27087fc_1 1002 KB conda-forge
openssl-3.0.2 | h166bdaf_1 2.9 MB conda-forge
python-3.7.12 |hf930737_100_cpython 57.3 MB conda-forge
python_abi-3.7 | 2_cp37m 4 KB conda-forge
readline-8.1 | h46c0cb4_0 295 KB conda-forge
sqlite-3.38.3 | h4ff8645_0 1.5 MB conda-forge
tk-8.6.12 | h27826a3_0 3.3 MB conda-forge
xz-5.2.5 | h516909a_1 343 KB conda-forge
zlib-1.2.11 | h166bdaf_1014 88 KB conda-forge
------------------------------------------------------------
Total: 77.2 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
libgomp conda-forge/linux-64::libgomp-11.2.0-h1d223b6_16
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libzlib conda-forge/linux-64::libzlib-1.2.11-h166bdaf_1014
python_abi conda-forge/linux-64::python_abi-3.7-2_cp37m
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2019.1.23-0 --> conda-forge::ca-certificates-2021.10.8-ha878542_0
certifi pkgs/main::certifi-2019.3.9-py37_0 --> conda-forge::certifi-2021.10.8-py37h89c1867_2
cffi pkgs/main::cffi-1.12.2-py37h2e261b9_1 --> conda-forge::cffi-1.15.0-py37h036bc23_0
cryptography 2.6.1-py37h1ba5d50_0 --> 36.0.0-py37h9ce1e76_0
libffi pkgs/main::libffi-3.2.1-hd88cf55_4 --> conda-forge::libffi-3.4.2-h7f98852_5
libgcc-ng pkgs/main::libgcc-ng-8.2.0-hdf63c60_1 --> conda-forge::libgcc-ng-11.2.0-h1d223b6_16
libstdcxx-ng pkgs/main::libstdcxx-ng-8.2.0-hdf63c6~ --> conda-forge::libstdcxx-ng-11.2.0-he4da1e4_16
ncurses pkgs/main::ncurses-6.1-he6710b0_1 --> conda-forge::ncurses-6.3-h27087fc_1
openssl pkgs/main::openssl-1.1.1b-h7b6447c_1 --> conda-forge::openssl-3.0.2-h166bdaf_1
python pkgs/main::python-3.7.3-h0371630_0 --> conda-forge::python-3.7.12-hf930737_100_cpython
readline pkgs/main::readline-7.0-h7b6447c_5 --> conda-forge::readline-8.1-h46c0cb4_0
sqlite pkgs/main::sqlite-3.27.2-h7b6447c_0 --> conda-forge::sqlite-3.38.3-h4ff8645_0
tk pkgs/main::tk-8.6.8-hbc83047_0 --> conda-forge::tk-8.6.12-h27826a3_0
xz pkgs/main::xz-5.2.4-h14c3975_4 --> conda-forge::xz-5.2.5-h516909a_1
zlib pkgs/main::zlib-1.2.11-h7b6447c_3 --> conda-forge::zlib-1.2.11-h166bdaf_1014
The following packages will be SUPERSEDED by a higher-priority channel:
conda pkgs/main --> conda-forge
Downloading and Extracting Packages
conda-4.6.14 | 2.1 MB | | 0%
conda-4.6.14 | 2.1 MB | | 1%
conda-4.6.14 | 2.1 MB | #4 | 15%
conda-4.6.14 | 2.1 MB | #8 | 19%
conda-4.6.14 | 2.1 MB | ######6 | 66%
conda-4.6.14 | 2.1 MB | ########3 | 83%
conda-4.6.14 | 2.1 MB | #########8 | 99%
conda-4.6.14 | 2.1 MB | ########## | 100%
cffi-1.15.0 | 225 KB | | 0%
cffi-1.15.0 | 225 KB | #########8 | 98%
cffi-1.15.0 | 225 KB | ########## | 100%
_libgcc_mutex-0.1 | 3 KB | | 0%
_libgcc_mutex-0.1 | 3 KB | ########## | 100%
ld_impl_linux-64-2.3 | 667 KB | | 0%
ld_impl_linux-64-2.3 | 667 KB | ####### | 70%
ld_impl_linux-64-2.3 | 667 KB | #########9 | 99%
ld_impl_linux-64-2.3 | 667 KB | ########## | 100%
_openmp_mutex-4.5 | 23 KB | | 0%
_openmp_mutex-4.5 | 23 KB | ########## | 100%
libnsl-2.0.0 | 31 KB | | 0%
libnsl-2.0.0 | 31 KB | ########## | 100%
readline-8.1 | 295 KB | | 0%
readline-8.1 | 295 KB | ########1 | 82%
readline-8.1 | 295 KB | ########## | 100%
xz-5.2.5 | 343 KB | | 0%
xz-5.2.5 | 343 KB | ########5 | 85%
xz-5.2.5 | 343 KB | ########## | 100%
sqlite-3.38.3 | 1.5 MB | | 0%
sqlite-3.38.3 | 1.5 MB | #6 | 17%
sqlite-3.38.3 | 1.5 MB | #######5 | 76%
sqlite-3.38.3 | 1.5 MB | #########6 | 97%
sqlite-3.38.3 | 1.5 MB | ########## | 100%
cryptography-36.0.0 | 1.5 MB | | 0%
cryptography-36.0.0 | 1.5 MB | ###5 | 36%
cryptography-36.0.0 | 1.5 MB | #######7 | 78%
cryptography-36.0.0 | 1.5 MB | #########6 | 96%
cryptography-36.0.0 | 1.5 MB | ########## | 100%
libgcc-ng-11.2.0 | 902 KB | | 0%
libgcc-ng-11.2.0 | 902 KB | ###7 | 37%
libgcc-ng-11.2.0 | 902 KB | #########2 | 92%
libgcc-ng-11.2.0 | 902 KB | ########## | 100%
libffi-3.4.2 | 57 KB | | 0%
libffi-3.4.2 | 57 KB | ########## | 100%
ncurses-6.3 | 1002 KB | | 0%
ncurses-6.3 | 1002 KB | #### | 41%
ncurses-6.3 | 1002 KB | ########1 | 82%
ncurses-6.3 | 1002 KB | ########## | 100%
libgomp-11.2.0 | 428 KB | | 0%
libgomp-11.2.0 | 428 KB | 2 | 3%
libgomp-11.2.0 | 428 KB | ########## | 100%
libzlib-1.2.11 | 60 KB | | 0%
libzlib-1.2.11 | 60 KB | ########## | 100%
python-3.7.12 | 57.3 MB | | 0%
python-3.7.12 | 57.3 MB | | 0%
python-3.7.12 | 57.3 MB | 1 | 2%
python-3.7.12 | 57.3 MB | 3 | 4%
python-3.7.12 | 57.3 MB | 5 | 5%
python-3.7.12 | 57.3 MB | 7 | 7%
python-3.7.12 | 57.3 MB | 8 | 9%
python-3.7.12 | 57.3 MB | # | 10%
python-3.7.12 | 57.3 MB | #1 | 12%
python-3.7.12 | 57.3 MB | #3 | 14%
python-3.7.12 | 57.3 MB | #5 | 15%
python-3.7.12 | 57.3 MB | #7 | 17%
python-3.7.12 | 57.3 MB | #8 | 19%
python-3.7.12 | 57.3 MB | ## | 21%
python-3.7.12 | 57.3 MB | ##2 | 22%
python-3.7.12 | 57.3 MB | ##3 | 24%
python-3.7.12 | 57.3 MB | ##5 | 26%
python-3.7.12 | 57.3 MB | ##7 | 27%
python-3.7.12 | 57.3 MB | ##9 | 29%
python-3.7.12 | 57.3 MB | ### | 31%
python-3.7.12 | 57.3 MB | ###2 | 32%
python-3.7.12 | 57.3 MB | ###4 | 34%
python-3.7.12 | 57.3 MB | ###5 | 36%
python-3.7.12 | 57.3 MB | ###7 | 38%
python-3.7.12 | 57.3 MB | ###9 | 39%
python-3.7.12 | 57.3 MB | #### | 41%
python-3.7.12 | 57.3 MB | ####2 | 43%
python-3.7.12 | 57.3 MB | ####4 | 44%
python-3.7.12 | 57.3 MB | ####6 | 46%
python-3.7.12 | 57.3 MB | ####7 | 48%
python-3.7.12 | 57.3 MB | ####9 | 50%
python-3.7.12 | 57.3 MB | #####1 | 51%
python-3.7.12 | 57.3 MB | #####2 | 53%
python-3.7.12 | 57.3 MB | #####4 | 55%
python-3.7.12 | 57.3 MB | #####6 | 56%
python-3.7.12 | 57.3 MB | #####8 | 58%
python-3.7.12 | 57.3 MB | #####9 | 60%
python-3.7.12 | 57.3 MB | ######1 | 61%
python-3.7.12 | 57.3 MB | ######3 | 63%
python-3.7.12 | 57.3 MB | ######4 | 65%
python-3.7.12 | 57.3 MB | ######6 | 67%
python-3.7.12 | 57.3 MB | ######8 | 68%
python-3.7.12 | 57.3 MB | ######9 | 70%
python-3.7.12 | 57.3 MB | #######1 | 72%
python-3.7.12 | 57.3 MB | #######3 | 73%
python-3.7.12 | 57.3 MB | #######5 | 75%
python-3.7.12 | 57.3 MB | #######6 | 77%
python-3.7.12 | 57.3 MB | #######7 | 78%
python-3.7.12 | 57.3 MB | #######8 | 79%
python-3.7.12 | 57.3 MB | #######9 | 80%
python-3.7.12 | 57.3 MB | ######## | 80%
python-3.7.12 | 57.3 MB | ######## | 81%
python-3.7.12 | 57.3 MB | ########1 | 81%
python-3.7.12 | 57.3 MB | ########2 | 82%
python-3.7.12 | 57.3 MB | ########2 | 83%
python-3.7.12 | 57.3 MB | ########3 | 83%
python-3.7.12 | 57.3 MB | ########3 | 84%
python-3.7.12 | 57.3 MB | ########4 | 85%
python-3.7.12 | 57.3 MB | ########5 | 85%
python-3.7.12 | 57.3 MB | ########5 | 86%
python-3.7.12 | 57.3 MB | ########6 | 87%
python-3.7.12 | 57.3 MB | ########7 | 87%
python-3.7.12 | 57.3 MB | ########7 | 88%
python-3.7.12 | 57.3 MB | ########8 | 88%
python-3.7.12 | 57.3 MB | ########8 | 89%
python-3.7.12 | 57.3 MB | ########9 | 89%
python-3.7.12 | 57.3 MB | ########9 | 90%
python-3.7.12 | 57.3 MB | ######### | 90%
python-3.7.12 | 57.3 MB | ######### | 91%
python-3.7.12 | 57.3 MB | #########1 | 91%
python-3.7.12 | 57.3 MB | #########1 | 92%
python-3.7.12 | 57.3 MB | #########2 | 92%
python-3.7.12 | 57.3 MB | #########2 | 93%
python-3.7.12 | 57.3 MB | #########3 | 93%
python-3.7.12 | 57.3 MB | #########4 | 94%
python-3.7.12 | 57.3 MB | #########4 | 95%
python-3.7.12 | 57.3 MB | #########5 | 95%
python-3.7.12 | 57.3 MB | #########5 | 96%
python-3.7.12 | 57.3 MB | #########6 | 96%
python-3.7.12 | 57.3 MB | #########6 | 97%
python-3.7.12 | 57.3 MB | #########7 | 97%
python-3.7.12 | 57.3 MB | #########7 | 98%
python-3.7.12 | 57.3 MB | #########8 | 98%
python-3.7.12 | 57.3 MB | #########8 | 98%
python-3.7.12 | 57.3 MB | #########8 | 99%
python-3.7.12 | 57.3 MB | #########9 | 99%
python-3.7.12 | 57.3 MB | #########9 | 100%
python-3.7.12 | 57.3 MB | ########## | 100%
tk-8.6.12 | 3.3 MB | | 0%
tk-8.6.12 | 3.3 MB | 5 | 6%
tk-8.6.12 | 3.3 MB | #7 | 17%
tk-8.6.12 | 3.3 MB | ##8 | 29%
tk-8.6.12 | 3.3 MB | #### | 41%
tk-8.6.12 | 3.3 MB | ######6 | 66%
tk-8.6.12 | 3.3 MB | #######9 | 80%
tk-8.6.12 | 3.3 MB | #########2 | 92%
tk-8.6.12 | 3.3 MB | ########## | 100%
openssl-3.0.2 | 2.9 MB | | 0%
openssl-3.0.2 | 2.9 MB | 6 | 7%
openssl-3.0.2 | 2.9 MB | ###7 | 37%
openssl-3.0.2 | 2.9 MB | ######6 | 66%
openssl-3.0.2 | 2.9 MB | ########2 | 82%
openssl-3.0.2 | 2.9 MB | #########6 | 97%
openssl-3.0.2 | 2.9 MB | ########## | 100%
zlib-1.2.11 | 88 KB | | 0%
zlib-1.2.11 | 88 KB | ########## | 100%
libstdcxx-ng-11.2.0 | 4.2 MB | | 0%
libstdcxx-ng-11.2.0 | 4.2 MB | 9 | 10%
libstdcxx-ng-11.2.0 | 4.2 MB | ###3 | 33%
libstdcxx-ng-11.2.0 | 4.2 MB | #####4 | 55%
libstdcxx-ng-11.2.0 | 4.2 MB | #######5 | 75%
libstdcxx-ng-11.2.0 | 4.2 MB | ######### | 90%
libstdcxx-ng-11.2.0 | 4.2 MB | ########## | 100%
python_abi-3.7 | 4 KB | | 0%
python_abi-3.7 | 4 KB | ########## | 100%
ca-certificates-2021 | 139 KB | | 0%
ca-certificates-2021 | 139 KB | ########## | 100%
certifi-2021.10.8 | 145 KB | | 0%
certifi-2021.10.8 | 145 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

==> WARNING: A newer version of conda exists. <==
current version: 4.6.14
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata: ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/simple_use_case/cwl/cwltool_deps/_conda/envs/mulled-v1-0ce05ecb456bbb49cfed8a04aab86828a650d9a0a20aa7a9a5ce72b5c3a05956
added / updated specs:
- gmsh==4.6.0=hd134328_0
- meshio==5.0.5=pyhd8ed1ab_0
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | h7f98852_4 484 KB conda-forge
c-ares-1.18.1 | h7f98852_0 113 KB conda-forge
cached-property-1.5.2 | hd8ed1ab_1 4 KB conda-forge
cached_property-1.5.2 | pyha770c72_1 11 KB conda-forge
cftime-1.6.0 | py310hde88566_1 220 KB conda-forge
curl-7.83.0 | h2283fc2_0 89 KB conda-forge
expat-2.4.8 | h27087fc_0 187 KB conda-forge
fontconfig-2.14.0 | h8e229c2_0 305 KB conda-forge
freetype-2.10.4 | h0708190_1 890 KB conda-forge
gmp-6.2.1 | h58526e2_0 806 KB conda-forge
gmsh-4.6.0 | hd134328_0 97.2 MB conda-forge
h5py-3.6.0 |nompi_py310he751f51_100 6.7 MB conda-forge
hdf4-4.2.15 | h10796ff_3 950 KB conda-forge
hdf5-1.12.1 |nompi_h4df4325_104 3.6 MB conda-forge
importlib-metadata-4.11.3 | py310hff52083_1 33 KB conda-forge
importlib_metadata-4.11.3 | hd8ed1ab_1 4 KB conda-forge
jpeg-9e | h166bdaf_1 268 KB conda-forge
keyutils-1.6.1 | h166bdaf_0 115 KB conda-forge
krb5-1.19.3 | h08a2579_0 1.4 MB conda-forge
libblas-3.9.0 |14_linux64_openblas 12 KB conda-forge
libcblas-3.9.0 |14_linux64_openblas 12 KB conda-forge
libcurl-7.83.0 | h2283fc2_0 343 KB conda-forge
libedit-3.1.20191231 | he28a2e2_2 121 KB conda-forge
libev-4.33 | h516909a_1 104 KB conda-forge
libgfortran-ng-11.2.0 | h69a702a_16 23 KB conda-forge
libgfortran5-11.2.0 | h5c6108e_16 1.7 MB conda-forge
libglu-9.0.0 | he1b5a44_1001 413 KB conda-forge
liblapack-3.9.0 |14_linux64_openblas 12 KB conda-forge
libnetcdf-4.8.1 |nompi_h329d8a1_102 1.5 MB conda-forge
libnghttp2-1.47.0 | he49606f_0 824 KB conda-forge
libopenblas-0.3.20 |pthreads_h78a6416_0 10.1 MB conda-forge
libpng-1.6.37 | h21135ba_2 306 KB conda-forge
libssh2-1.10.0 | ha35d2d1_2 233 KB conda-forge
libuuid-2.32.1 | h7f98852_1000 28 KB conda-forge
libxcb-1.13 | h7f98852_1004 391 KB conda-forge
libzip-1.8.0 | h1c5bbd1_1 126 KB conda-forge
meshio-5.0.5 | pyhd8ed1ab_0 438 KB conda-forge
netcdf4-1.5.8 |nompi_py310hd7ca5b8_101 2.7 MB conda-forge
npx-0.1.1 | pyhd8ed1ab_0 13 KB conda-forge
numpy-1.22.3 | py310h4ef5377_2 6.8 MB conda-forge
occt-7.4.0 | h9121d39_3 28.1 MB conda-forge
pip-22.0.4 | pyhd8ed1ab_0 1.5 MB conda-forge
pthread-stubs-0.4 | h36c2ea0_1001 5 KB conda-forge
python-3.10.4 |h2660328_0_cpython 28.6 MB conda-forge
python_abi-3.10 | 2_cp310 4 KB conda-forge
setuptools-62.1.0 | py310hff52083_0 1.3 MB conda-forge
tbb-2020.2 | h4bd325d_4 1.5 MB conda-forge
tzdata-2022a | h191b570_0 121 KB conda-forge
wheel-0.37.1 | pyhd8ed1ab_0 31 KB conda-forge
xorg-fixesproto-5.0 | h7f98852_1002 9 KB conda-forge
xorg-kbproto-1.0.7 | h7f98852_1002 27 KB conda-forge
xorg-libice-1.0.10 | h7f98852_0 58 KB conda-forge
xorg-libsm-1.2.3 | hd9c2040_1000 26 KB conda-forge
xorg-libx11-1.7.2 | h7f98852_0 941 KB conda-forge
xorg-libxau-1.0.9 | h7f98852_0 13 KB conda-forge
xorg-libxdmcp-1.1.3 | h7f98852_0 19 KB conda-forge
xorg-libxext-1.3.4 | h7f98852_1 54 KB conda-forge
xorg-libxfixes-5.0.3 | h7f98852_1004 18 KB conda-forge
xorg-libxmu-1.1.3 | h7f98852_0 90 KB conda-forge
xorg-libxrender-0.9.10 | h7f98852_1003 32 KB conda-forge
xorg-libxt-1.2.1 | h7f98852_2 375 KB conda-forge
xorg-renderproto-0.11.1 | h7f98852_1002 9 KB conda-forge
xorg-xextproto-7.3.0 | h7f98852_1002 28 KB conda-forge
xorg-xproto-7.0.31 | h7f98852_1007 73 KB conda-forge
zipp-3.8.0 | pyhd8ed1ab_0 12 KB conda-forge
------------------------------------------------------------
Total: 202.3 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
c-ares conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
ca-certificates conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
cftime conda-forge/linux-64::cftime-1.6.0-py310hde88566_1
curl conda-forge/linux-64::curl-7.83.0-h2283fc2_0
expat conda-forge/linux-64::expat-2.4.8-h27087fc_0
fontconfig conda-forge/linux-64::fontconfig-2.14.0-h8e229c2_0
freetype conda-forge/linux-64::freetype-2.10.4-h0708190_1
gmp conda-forge/linux-64::gmp-6.2.1-h58526e2_0
gmsh conda-forge/linux-64::gmsh-4.6.0-hd134328_0
h5py conda-forge/linux-64::h5py-3.6.0-nompi_py310he751f51_100
hdf4 conda-forge/linux-64::hdf4-4.2.15-h10796ff_3
hdf5 conda-forge/linux-64::hdf5-1.12.1-nompi_h4df4325_104
importlib-metadata conda-forge/linux-64::importlib-metadata-4.11.3-py310hff52083_1
importlib_metadata conda-forge/noarch::importlib_metadata-4.11.3-hd8ed1ab_1
jpeg conda-forge/linux-64::jpeg-9e-h166bdaf_1
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.19.3-h08a2579_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
libblas conda-forge/linux-64::libblas-3.9.0-14_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-14_linux64_openblas
libcurl conda-forge/linux-64::libcurl-7.83.0-h2283fc2_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_16
libgfortran-ng conda-forge/linux-64::libgfortran-ng-11.2.0-h69a702a_16
libgfortran5 conda-forge/linux-64::libgfortran5-11.2.0-h5c6108e_16
libglu conda-forge/linux-64::libglu-9.0.0-he1b5a44_1001
libgomp conda-forge/linux-64::libgomp-11.2.0-h1d223b6_16
liblapack conda-forge/linux-64::liblapack-3.9.0-14_linux64_openblas
libnetcdf conda-forge/linux-64::libnetcdf-4.8.1-nompi_h329d8a1_102
libnghttp2 conda-forge/linux-64::libnghttp2-1.47.0-he49606f_0
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libopenblas conda-forge/linux-64::libopenblas-0.3.20-pthreads_h78a6416_0
libpng conda-forge/linux-64::libpng-1.6.37-h21135ba_2
libssh2 conda-forge/linux-64::libssh2-1.10.0-ha35d2d1_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_16
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libxcb conda-forge/linux-64::libxcb-1.13-h7f98852_1004
libzip conda-forge/linux-64::libzip-1.8.0-h1c5bbd1_1
libzlib conda-forge/linux-64::libzlib-1.2.11-h166bdaf_1014
meshio conda-forge/noarch::meshio-5.0.5-pyhd8ed1ab_0
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
netcdf4 conda-forge/linux-64::netcdf4-1.5.8-nompi_py310hd7ca5b8_101
npx conda-forge/noarch::npx-0.1.1-pyhd8ed1ab_0
numpy conda-forge/linux-64::numpy-1.22.3-py310h4ef5377_2
occt conda-forge/linux-64::occt-7.4.0-h9121d39_3
openssl conda-forge/linux-64::openssl-3.0.2-h166bdaf_1
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
python conda-forge/linux-64::python-3.10.4-h2660328_0_cpython
python_abi conda-forge/linux-64::python_abi-3.10-2_cp310
readline conda-forge/linux-64::readline-8.1-h46c0cb4_0
setuptools conda-forge/linux-64::setuptools-62.1.0-py310hff52083_0
sqlite conda-forge/linux-64::sqlite-3.38.3-h4ff8645_0
tbb conda-forge/linux-64::tbb-2020.2-h4bd325d_4
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
tzdata conda-forge/noarch::tzdata-2022a-h191b570_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xorg-fixesproto conda-forge/linux-64::xorg-fixesproto-5.0-h7f98852_1002
xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002
xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h7f98852_0
xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-hd9c2040_1000
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.7.2-h7f98852_0
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h7f98852_1
xorg-libxfixes conda-forge/linux-64::xorg-libxfixes-5.0.3-h7f98852_1004
xorg-libxmu conda-forge/linux-64::xorg-libxmu-1.1.3-h7f98852_0
xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h7f98852_1003
xorg-libxt conda-forge/linux-64::xorg-libxt-1.2.1-h7f98852_2
xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002
xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h7f98852_1002
xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
zipp conda-forge/noarch::zipp-3.8.0-pyhd8ed1ab_0
zlib conda-forge/linux-64::zlib-1.2.11-h166bdaf_1014
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
/tmp/simple_use_case/cwl/cwltool_deps/_conda/lib/python3.7/site-packages/cryptography/hazmat/backends/openssl/x509.py:17: CryptographyDeprecationWarning: This version of cryptography contains a temporary pyOpenSSL fallback path. Upgrade pyOpenSSL now.
utils.DeprecatedIn35,
Info : Running 'gmsh -setnumber domain_size 1.0 -2 /tmp/pfls8gqy/stgd8228832-2845-49a1-8043-3122d857daaf/unit_square.geo -o mesh.msh' [Gmsh 4.6.0, 1 node, max. 1 thread]
Info : Started on Tue May 3 17:22:23 2022
Info : Reading '/tmp/pfls8gqy/stgd8228832-2845-49a1-8043-3122d857daaf/unit_square.geo'...
Used domain size: 1.000000
Used mesh size: 0.250000
Info : Done reading '/tmp/pfls8gqy/stgd8228832-2845-49a1-8043-3122d857daaf/unit_square.geo'
Info : Meshing 1D...
Info : [ 0%] Meshing curve 1 (Line)
Info : [ 30%] Meshing curve 2 (Line)
Info : [ 50%] Meshing curve 3 (Line)
Info : [ 80%] Meshing curve 4 (Line)
Info : Done meshing 1D (Wall 0.00143099s, CPU 0.006133s)
Info : Meshing 2D...
Info : Meshing surface 1 (Plane, Frontal-Delaunay)
Info : Done meshing 2D (Wall 0.023011s, CPU 0.064198s)
Info : 98 nodes 198 elements
Info : Writing 'mesh.msh'...
Info : Done writing 'mesh.msh'
Info : Stopped on Tue May 3 17:22:23 2022 (From start: Wall 0.0393472s, CPU 0.163573s)
INFO [job make_mesh] completed success
DEBUG [job make_mesh] outputs {
"mesh": {
"location": "file:///tmp/porwxmx7/mesh.msh",
"basename": "mesh.msh",
"nameroot": "mesh",
"nameext": ".msh",
"class": "File",
"checksum": "sha1$c723355fdbec0cfe31a9bfa51009493b99b71e88",
"size": 6380,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step make_mesh] produced output {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#make_mesh/mesh": {
"location": "file:///tmp/porwxmx7/mesh.msh",
"basename": "mesh.msh",
"nameroot": "mesh",
"nameext": ".msh",
"class": "File",
"checksum": "sha1$c723355fdbec0cfe31a9bfa51009493b99b71e88",
"size": 6380,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step make_mesh] completed success
DEBUG [job make_mesh] Removing input staging directory /tmp/pfls8gqy
DEBUG [job make_mesh] Removing temporary directory /tmp/n9l5b6o2
DEBUG [workflow ] job step file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#plot_over_line not ready
DEBUG [workflow ] job step file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#prepare_paper_macros not ready
DEBUG [workflow ] job step file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#compile_paper not ready
INFO [workflow ] starting step convert_mesh
DEBUG [step convert_mesh] job input {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#convert_mesh/inputmesh": {
"location": "file:///tmp/porwxmx7/mesh.msh",
"basename": "mesh.msh",
"nameroot": "mesh",
"nameext": ".msh",
"class": "File",
"checksum": "sha1$c723355fdbec0cfe31a9bfa51009493b99b71e88",
"size": 6380,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step convert_mesh] evaluated job input to {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#convert_mesh/inputmesh": {
"location": "file:///tmp/porwxmx7/mesh.msh",
"basename": "mesh.msh",
"nameroot": "mesh",
"nameext": ".msh",
"class": "File",
"checksum": "sha1$c723355fdbec0cfe31a9bfa51009493b99b71e88",
"size": 6380,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step convert_mesh] start
DEBUG [job convert_mesh] initializing from file:///tmp/simple_use_case/cwl/convert_msh_to_xdmf.cwl as part of step convert_mesh
DEBUG [job convert_mesh] {
"inputmesh": {
"location": "file:///tmp/porwxmx7/mesh.msh",
"basename": "mesh.msh",
"nameroot": "mesh",
"nameext": ".msh",
"class": "File",
"checksum": "sha1$c723355fdbec0cfe31a9bfa51009493b99b71e88",
"size": 6380,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [job convert_mesh] path mappings is {
"file:///tmp/porwxmx7/mesh.msh": [
"/tmp/porwxmx7/mesh.msh",
"/tmp/d21eu_75/stg1d514e64-089a-4ce9-aefb-08ea328ead8e/mesh.msh",
"File",
true
]
}
DEBUG [job convert_mesh] command line bindings is [
{
"position": [
-1000000,
0
],
"datum": "meshio"
},
{
"position": [
-1000000,
1
],
"datum": "convert"
},
{
"position": [
0,
0
],
"valueFrom": "$(inputs.inputmesh.path)"
},
{
"position": [
0,
1
],
"datum": "mesh_converted.xdmf"
}
]
DEBUG [job convert_mesh] initial work dir {}
INFO [job convert_mesh] /tmp/6d5f4j4s$ meshio \
convert \
/tmp/d21eu_75/stg1d514e64-089a-4ce9-aefb-08ea328ead8e/mesh.msh \
mesh_converted.xdmf
Collecting package metadata: ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/simple_use_case/cwl/cwltool_deps/_conda/envs/[email protected]=pyhd8ed1ab_0
added / updated specs:
- meshio==5.0.5=pyhd8ed1ab_0
The following packages will be downloaded:
package | build
---------------------------|-----------------
cftime-1.6.0 | py39hd257fcd_1 220 KB conda-forge
h5py-3.6.0 |nompi_py39h7e08c79_100 1.3 MB conda-forge
importlib-metadata-4.11.3 | py39hf3d152e_1 33 KB conda-forge
netcdf4-1.5.8 |nompi_py39h64b754b_101 560 KB conda-forge
numpy-1.20.3 | py39hdbf815f_0 5.8 MB conda-forge
python-3.9.12 |h2660328_1_cpython 26.6 MB conda-forge
python_abi-3.9 | 2_cp39 4 KB conda-forge
setuptools-62.1.0 | py39hf3d152e_0 1.3 MB conda-forge
------------------------------------------------------------
Total: 35.8 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
c-ares conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
ca-certificates conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
cftime conda-forge/linux-64::cftime-1.6.0-py39hd257fcd_1
curl conda-forge/linux-64::curl-7.83.0-h2283fc2_0
h5py conda-forge/linux-64::h5py-3.6.0-nompi_py39h7e08c79_100
hdf4 conda-forge/linux-64::hdf4-4.2.15-h10796ff_3
hdf5 conda-forge/linux-64::hdf5-1.12.1-nompi_h4df4325_104
importlib-metadata conda-forge/linux-64::importlib-metadata-4.11.3-py39hf3d152e_1
importlib_metadata conda-forge/noarch::importlib_metadata-4.11.3-hd8ed1ab_1
jpeg conda-forge/linux-64::jpeg-9e-h166bdaf_1
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.19.3-h08a2579_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
libblas conda-forge/linux-64::libblas-3.9.0-14_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-14_linux64_openblas
libcurl conda-forge/linux-64::libcurl-7.83.0-h2283fc2_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_16
libgfortran-ng conda-forge/linux-64::libgfortran-ng-11.2.0-h69a702a_16
libgfortran5 conda-forge/linux-64::libgfortran5-11.2.0-h5c6108e_16
libgomp conda-forge/linux-64::libgomp-11.2.0-h1d223b6_16
liblapack conda-forge/linux-64::liblapack-3.9.0-14_linux64_openblas
libnetcdf conda-forge/linux-64::libnetcdf-4.8.1-nompi_h329d8a1_102
libnghttp2 conda-forge/linux-64::libnghttp2-1.47.0-he49606f_0
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libopenblas conda-forge/linux-64::libopenblas-0.3.20-pthreads_h78a6416_0
libssh2 conda-forge/linux-64::libssh2-1.10.0-ha35d2d1_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_16
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libzip conda-forge/linux-64::libzip-1.8.0-h1c5bbd1_1
libzlib conda-forge/linux-64::libzlib-1.2.11-h166bdaf_1014
meshio conda-forge/noarch::meshio-5.0.5-pyhd8ed1ab_0
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
netcdf4 conda-forge/linux-64::netcdf4-1.5.8-nompi_py39h64b754b_101
npx conda-forge/noarch::npx-0.1.1-pyhd8ed1ab_0
numpy conda-forge/linux-64::numpy-1.20.3-py39hdbf815f_0
openssl conda-forge/linux-64::openssl-3.0.2-h166bdaf_1
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
python_abi conda-forge/linux-64::python_abi-3.9-2_cp39
readline conda-forge/linux-64::readline-8.1-h46c0cb4_0
setuptools conda-forge/linux-64::setuptools-62.1.0-py39hf3d152e_0
sqlite conda-forge/linux-64::sqlite-3.38.3-h4ff8645_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
tzdata conda-forge/noarch::tzdata-2022a-h191b570_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
zipp conda-forge/noarch::zipp-3.8.0-pyhd8ed1ab_0
zlib conda-forge/linux-64::zlib-1.2.11-h166bdaf_1014
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
/tmp/simple_use_case/cwl/cwltool_deps/_conda/lib/python3.7/site-packages/cryptography/hazmat/backends/openssl/x509.py:17: CryptographyDeprecationWarning: This version of cryptography contains a temporary pyOpenSSL fallback path. Upgrade pyOpenSSL now.
utils.DeprecatedIn35,
INFO [job convert_mesh] completed success
DEBUG [job convert_mesh] outputs {
"outputmesh": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.xdmf",
"basename": "mesh_converted.xdmf",
"nameroot": "mesh_converted",
"nameext": ".xdmf",
"class": "File",
"checksum": "sha1$1175d8d621317a8f9c763d65a2dc04faaba1e54a",
"size": 969,
"http://commonwl.org/cwltool#generation": 0
},
"outputmeshdata": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.h5",
"basename": "mesh_converted.h5",
"nameroot": "mesh_converted",
"nameext": ".h5",
"class": "File",
"checksum": "sha1$ac00b0d4862b464f5af59a5e262098c6eb24ee7d",
"size": 16576,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step convert_mesh] produced output {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#convert_mesh/outputmesh": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.xdmf",
"basename": "mesh_converted.xdmf",
"nameroot": "mesh_converted",
"nameext": ".xdmf",
"class": "File",
"checksum": "sha1$1175d8d621317a8f9c763d65a2dc04faaba1e54a",
"size": 969,
"http://commonwl.org/cwltool#generation": 0
},
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#convert_mesh/outputmeshdata": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.h5",
"basename": "mesh_converted.h5",
"nameroot": "mesh_converted",
"nameext": ".h5",
"class": "File",
"checksum": "sha1$ac00b0d4862b464f5af59a5e262098c6eb24ee7d",
"size": 16576,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step convert_mesh] completed success
DEBUG [job convert_mesh] Removing input staging directory /tmp/d21eu_75
DEBUG [job convert_mesh] Removing temporary directory /tmp/0x0017l5
INFO [workflow ] starting step run_simulation
DEBUG [step run_simulation] job input {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#run_simulation/h5meshfile": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.h5",
"basename": "mesh_converted.h5",
"nameroot": "mesh_converted",
"nameext": ".h5",
"class": "File",
"checksum": "sha1$ac00b0d4862b464f5af59a5e262098c6eb24ee7d",
"size": 16576,
"http://commonwl.org/cwltool#generation": 0
},
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#run_simulation/xdmfmeshfile": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.xdmf",
"basename": "mesh_converted.xdmf",
"nameroot": "mesh_converted",
"nameext": ".xdmf",
"class": "File",
"checksum": "sha1$1175d8d621317a8f9c763d65a2dc04faaba1e54a",
"size": 969,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step run_simulation] evaluated job input to {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#run_simulation/h5meshfile": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.h5",
"basename": "mesh_converted.h5",
"nameroot": "mesh_converted",
"nameext": ".h5",
"class": "File",
"checksum": "sha1$ac00b0d4862b464f5af59a5e262098c6eb24ee7d",
"size": 16576,
"http://commonwl.org/cwltool#generation": 0
},
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#run_simulation/xdmfmeshfile": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.xdmf",
"basename": "mesh_converted.xdmf",
"nameroot": "mesh_converted",
"nameext": ".xdmf",
"class": "File",
"checksum": "sha1$1175d8d621317a8f9c763d65a2dc04faaba1e54a",
"size": 969,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step run_simulation] start
DEBUG [job run_simulation] initializing from file:///tmp/simple_use_case/cwl/run_dolfin.cwl as part of step run_simulation
DEBUG [job run_simulation] {
"h5meshfile": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.h5",
"basename": "mesh_converted.h5",
"nameroot": "mesh_converted",
"nameext": ".h5",
"class": "File",
"checksum": "sha1$ac00b0d4862b464f5af59a5e262098c6eb24ee7d",
"size": 16576,
"http://commonwl.org/cwltool#generation": 0
},
"xdmfmeshfile": {
"location": "file:///tmp/6d5f4j4s/mesh_converted.xdmf",
"basename": "mesh_converted.xdmf",
"nameroot": "mesh_converted",
"nameext": ".xdmf",
"class": "File",
"checksum": "sha1$1175d8d621317a8f9c763d65a2dc04faaba1e54a",
"size": 969,
"http://commonwl.org/cwltool#generation": 0
},
"script": {
"class": "File",
"location": "file:///tmp/simple_use_case/source/poisson.py",
"basename": "poisson.py",
"nameroot": "poisson",
"nameext": ".py",
"size": 3206
}
}
DEBUG [job run_simulation] path mappings is {
"file:///tmp/6d5f4j4s/mesh_converted.h5": [
"/tmp/6d5f4j4s/mesh_converted.h5",
"/tmp/ktyym5s8/mesh_converted.h5",
"File",
false
],
"file:///tmp/simple_use_case/source/poisson.py": [
"/tmp/simple_use_case/source/poisson.py",
"/tmp/b744q5ut/stg1f89c746-07cf-4537-bb31-6909c81e4312/poisson.py",
"File",
true
],
"file:///tmp/6d5f4j4s/mesh_converted.xdmf": [
"/tmp/6d5f4j4s/mesh_converted.xdmf",
"/tmp/ktyym5s8/mesh_converted.xdmf",
"File",
false
]
}
DEBUG [job run_simulation] command line bindings is [
{
"position": [
-1000000,
0
],
"datum": "python3"
},
{
"position": [
0,
0
],
"valueFrom": "$(inputs.script)"
},
{
"position": [
0,
1
],
"datum": "--mesh"
},
{
"position": [
0,
2
],
"valueFrom": "$(inputs.xdmfmeshfile.path)"
},
{
"position": [
0,
3
],
"datum": "--degree"
},
{
"position": [
0,
4
],
"datum": "2"
},
{
"position": [
0,
5
],
"datum": "--output"
},
{
"position": [
0,
6
],
"datum": "result.pvd"
}
]
DEBUG [job run_simulation] initial work dir {
"file:///tmp/6d5f4j4s/mesh_converted.xdmf": [
"/tmp/6d5f4j4s/mesh_converted.xdmf",
"/tmp/ktyym5s8/mesh_converted.xdmf",
"File",
true
],
"file:///tmp/6d5f4j4s/mesh_converted.h5": [
"/tmp/6d5f4j4s/mesh_converted.h5",
"/tmp/ktyym5s8/mesh_converted.h5",
"File",
true
]
}
INFO [job run_simulation] /tmp/ktyym5s8$ python3 \
/tmp/b744q5ut/stg1f89c746-07cf-4537-bb31-6909c81e4312/poisson.py \
--mesh \
/tmp/ktyym5s8/mesh_converted.xdmf \
--degree \
2 \
--output \
result.pvd > /tmp/ktyym5s8/output.txt
Collecting package metadata: ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/simple_use_case/cwl/cwltool_deps/_conda/envs/[email protected]=py39hf3d152e_26
added / updated specs:
- fenics==2019.1.0=py39hf3d152e_26
The following packages will be downloaded:
package | build
---------------------------|-----------------
binutils_impl_linux-64-2.36.1| h193b22a_2 10.4 MB conda-forge
binutils_linux-64-2.36 | hf3e587d_9 24 KB conda-forge
boost-cpp-1.74.0 | h75c5d50_8 16.2 MB conda-forge
cmake-3.23.1 | h5432695_0 16.3 MB conda-forge
eigen-3.4.0 | h4bd325d_0 1.2 MB conda-forge
fenics-2019.1.0 | py39hf3d152e_26 11 KB conda-forge
fenics-dijitso-2019.1.0 | py39hf3d152e_26 63 KB conda-forge
fenics-dolfin-2019.1.0 | py39h68d5232_26 1.2 MB conda-forge
fenics-ffc-2019.1.0 | py39hf3d152e_26 462 KB conda-forge
fenics-fiat-2019.1.0 | py39hf3d152e_26 138 KB conda-forge
fenics-libdolfin-2019.1.0 | h12c0dc9_26 2.3 MB conda-forge
fenics-ufl-2019.1.0 | py39hf3d152e_26 337 KB conda-forge
fftw-3.3.10 |mpi_mpich_h8b92f0a_2 6.5 MB conda-forge
gcc_impl_linux-64-9.4.0 | h03d3576_16 43.4 MB conda-forge
gcc_linux-64-9.4.0 | h391b98a_9 25 KB conda-forge
gmpy2-2.1.2 | py39h78fa15d_0 781 KB conda-forge
gxx_impl_linux-64-9.4.0 | h03d3576_16 10.6 MB conda-forge
gxx_linux-64-9.4.0 | h0316aca_9 24 KB conda-forge
hdf5-1.10.6 |mpi_mpich_h996c276_1014 3.2 MB conda-forge
hypre-2.24.0 |mpi_mpich_h0faba72_0 1.8 MB conda-forge
icu-70.1 | h27087fc_0 13.5 MB conda-forge
kernel-headers_linux-64-2.6.32| he073ed8_15 707 KB conda-forge
krb5-1.19.3 | h3790be6_0 1.4 MB conda-forge
libcurl-7.83.0 | h7bff187_0 342 KB conda-forge
libgcc-devel_linux-64-9.4.0| hd854feb_16 4.0 MB conda-forge
libnghttp2-1.47.0 | h727a467_0 808 KB conda-forge
libsanitizer-9.4.0 | h79bfe98_16 6.9 MB conda-forge
libssh2-1.10.0 | ha56f1ee_2 233 KB conda-forge
libstdcxx-devel_linux-64-9.4.0| hd854feb_16 9.9 MB conda-forge
libuv-1.43.0 | h7f98852_0 1.0 MB conda-forge
lz4-c-1.9.3 | h9c3ff4c_1 179 KB conda-forge
metis-5.1.0 | h58526e2_1006 4.1 MB conda-forge
mpc-1.2.1 | h9f54685_0 106 KB conda-forge
mpfr-4.1.0 | h9202a9a_1 2.6 MB conda-forge
mpi-1.0 | mpich 4 KB conda-forge
mpi4py-3.1.3 | py39h32b9844_1 609 KB conda-forge
mpich-4.0.2 | h846660c_100 6.0 MB conda-forge
mpmath-1.2.1 | pyhd8ed1ab_0 437 KB conda-forge
mumps-include-5.2.1 | ha770c72_11 23 KB conda-forge
mumps-mpi-5.2.1 | h7ee95aa_11 3.3 MB conda-forge
numpy-1.22.3 | py39hc58783e_2 6.8 MB conda-forge
openssl-1.1.1n | h166bdaf_0 2.1 MB conda-forge
parmetis-4.0.3 | h2a9763c_1005 274 KB conda-forge
petsc-3.16.6 |real_h259f340_100 10.6 MB conda-forge
petsc4py-3.16.6 |real_h016f20b_100 1.1 MB conda-forge
pkg-config-0.29.2 | h36c2ea0_1008 120 KB conda-forge
pkgconfig-1.5.5 | py39hf3d152e_2 13 KB conda-forge
ptscotch-6.0.9 | hb499603_2 1.5 MB conda-forge
pybind11-2.8.1 | py39h1a9c180_1 160 KB conda-forge
pybind11-global-2.8.1 | py39h1a9c180_1 194 KB conda-forge
python-3.9.12 |h9a8a25e_1_cpython 26.7 MB conda-forge
rhash-1.4.1 | h7f98852_0 192 KB conda-forge
scalapack-2.2.0 | hd931219_1 2.2 MB conda-forge
scotch-6.0.9 | hb2e6521_2 1.3 MB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
slepc-3.16.1 |real_h7bbb3bb_101 3.8 MB conda-forge
slepc4py-3.16.1 |real_hd623573_100 417 KB conda-forge
suitesparse-5.10.1 | h9e50725_1 2.4 MB conda-forge
superlu-5.2.2 | h16cfea0_0 217 KB conda-forge
superlu_dist-7.2.0 | h25dcc4a_0 1.1 MB conda-forge
sympy-1.10.1 | py39hf3d152e_0 11.7 MB conda-forge
sysroot_linux-64-2.12 | he073ed8_15 31.4 MB conda-forge
tbb-2021.5.0 | h924138e_1 1.9 MB conda-forge
yaml-0.2.5 | h7f98852_2 87 KB conda-forge
zstd-1.5.2 | ha95c52a_0 458 KB conda-forge
------------------------------------------------------------
Total: 278.0 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.36.1-h193b22a_2
binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.36-hf3e587d_9
boost-cpp conda-forge/linux-64::boost-cpp-1.74.0-h75c5d50_8
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
c-ares conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
ca-certificates conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
cmake conda-forge/linux-64::cmake-3.23.1-h5432695_0
eigen conda-forge/linux-64::eigen-3.4.0-h4bd325d_0
expat conda-forge/linux-64::expat-2.4.8-h27087fc_0
fenics conda-forge/linux-64::fenics-2019.1.0-py39hf3d152e_26
fenics-dijitso conda-forge/linux-64::fenics-dijitso-2019.1.0-py39hf3d152e_26
fenics-dolfin conda-forge/linux-64::fenics-dolfin-2019.1.0-py39h68d5232_26
fenics-ffc conda-forge/linux-64::fenics-ffc-2019.1.0-py39hf3d152e_26
fenics-fiat conda-forge/linux-64::fenics-fiat-2019.1.0-py39hf3d152e_26
fenics-libdolfin conda-forge/linux-64::fenics-libdolfin-2019.1.0-h12c0dc9_26
fenics-ufl conda-forge/linux-64::fenics-ufl-2019.1.0-py39hf3d152e_26
fftw conda-forge/linux-64::fftw-3.3.10-mpi_mpich_h8b92f0a_2
gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-9.4.0-h03d3576_16
gcc_linux-64 conda-forge/linux-64::gcc_linux-64-9.4.0-h391b98a_9
gmp conda-forge/linux-64::gmp-6.2.1-h58526e2_0
gmpy2 conda-forge/linux-64::gmpy2-2.1.2-py39h78fa15d_0
gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-9.4.0-h03d3576_16
gxx_linux-64 conda-forge/linux-64::gxx_linux-64-9.4.0-h0316aca_9
hdf5 conda-forge/linux-64::hdf5-1.10.6-mpi_mpich_h996c276_1014
hypre conda-forge/linux-64::hypre-2.24.0-mpi_mpich_h0faba72_0
icu conda-forge/linux-64::icu-70.1-h27087fc_0
kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-he073ed8_15
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.19.3-h3790be6_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
libblas conda-forge/linux-64::libblas-3.9.0-14_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-14_linux64_openblas
libcurl conda-forge/linux-64::libcurl-7.83.0-h7bff187_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-devel_linu~ conda-forge/linux-64::libgcc-devel_linux-64-9.4.0-hd854feb_16
libgcc-ng conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_16
libgfortran-ng conda-forge/linux-64::libgfortran-ng-11.2.0-h69a702a_16
libgfortran5 conda-forge/linux-64::libgfortran5-11.2.0-h5c6108e_16
libgomp conda-forge/linux-64::libgomp-11.2.0-h1d223b6_16
liblapack conda-forge/linux-64::liblapack-3.9.0-14_linux64_openblas
libnghttp2 conda-forge/linux-64::libnghttp2-1.47.0-h727a467_0
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libopenblas conda-forge/linux-64::libopenblas-0.3.20-pthreads_h78a6416_0
libsanitizer conda-forge/linux-64::libsanitizer-9.4.0-h79bfe98_16
libssh2 conda-forge/linux-64::libssh2-1.10.0-ha56f1ee_2
libstdcxx-devel_l~ conda-forge/linux-64::libstdcxx-devel_linux-64-9.4.0-hd854feb_16
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_16
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libuv conda-forge/linux-64::libuv-1.43.0-h7f98852_0
libzlib conda-forge/linux-64::libzlib-1.2.11-h166bdaf_1014
lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_1
metis conda-forge/linux-64::metis-5.1.0-h58526e2_1006
mpc conda-forge/linux-64::mpc-1.2.1-h9f54685_0
mpfr conda-forge/linux-64::mpfr-4.1.0-h9202a9a_1
mpi conda-forge/linux-64::mpi-1.0-mpich
mpi4py conda-forge/linux-64::mpi4py-3.1.3-py39h32b9844_1
mpich conda-forge/linux-64::mpich-4.0.2-h846660c_100
mpmath conda-forge/noarch::mpmath-1.2.1-pyhd8ed1ab_0
mumps-include conda-forge/linux-64::mumps-include-5.2.1-ha770c72_11
mumps-mpi conda-forge/linux-64::mumps-mpi-5.2.1-h7ee95aa_11
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
numpy conda-forge/linux-64::numpy-1.22.3-py39hc58783e_2
openssl conda-forge/linux-64::openssl-1.1.1n-h166bdaf_0
parmetis conda-forge/linux-64::parmetis-4.0.3-h2a9763c_1005
petsc conda-forge/linux-64::petsc-3.16.6-real_h259f340_100
petsc4py conda-forge/linux-64::petsc4py-3.16.6-real_h016f20b_100
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
pkg-config conda-forge/linux-64::pkg-config-0.29.2-h36c2ea0_1008
pkgconfig conda-forge/linux-64::pkgconfig-1.5.5-py39hf3d152e_2
ptscotch conda-forge/linux-64::ptscotch-6.0.9-hb499603_2
pybind11 conda-forge/linux-64::pybind11-2.8.1-py39h1a9c180_1
pybind11-global conda-forge/linux-64::pybind11-global-2.8.1-py39h1a9c180_1
python conda-forge/linux-64::python-3.9.12-h9a8a25e_1_cpython
python_abi conda-forge/linux-64::python_abi-3.9-2_cp39
readline conda-forge/linux-64::readline-8.1-h46c0cb4_0
rhash conda-forge/linux-64::rhash-1.4.1-h7f98852_0
scalapack conda-forge/linux-64::scalapack-2.2.0-hd931219_1
scotch conda-forge/linux-64::scotch-6.0.9-hb2e6521_2
setuptools conda-forge/linux-64::setuptools-62.1.0-py39hf3d152e_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
slepc conda-forge/linux-64::slepc-3.16.1-real_h7bbb3bb_101
slepc4py conda-forge/linux-64::slepc4py-3.16.1-real_hd623573_100
sqlite conda-forge/linux-64::sqlite-3.38.3-h4ff8645_0
suitesparse conda-forge/linux-64::suitesparse-5.10.1-h9e50725_1
superlu conda-forge/linux-64::superlu-5.2.2-h16cfea0_0
superlu_dist conda-forge/linux-64::superlu_dist-7.2.0-h25dcc4a_0
sympy conda-forge/linux-64::sympy-1.10.1-py39hf3d152e_0
sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.12-he073ed8_15
tbb conda-forge/linux-64::tbb-2021.5.0-h924138e_1
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
tzdata conda-forge/noarch::tzdata-2022a-h191b570_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
yaml conda-forge/linux-64::yaml-0.2.5-h7f98852_2
zlib conda-forge/linux-64::zlib-1.2.11-h166bdaf_1014
zstd conda-forge/linux-64::zstd-1.5.2-ha95c52a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
/tmp/simple_use_case/cwl/cwltool_deps/_conda/lib/python3.7/site-packages/cryptography/hazmat/backends/openssl/x509.py:17: CryptographyDeprecationWarning: This version of cryptography contains a temporary pyOpenSSL fallback path. Upgrade pyOpenSSL now.
utils.DeprecatedIn35,
INFO [job run_simulation] completed success
DEBUG [job run_simulation] outputs {
"num_dofs": 357,
"resultpvd": {
"location": "file:///tmp/ktyym5s8/result.pvd",
"basename": "result.pvd",
"nameroot": "result",
"nameext": ".pvd",
"class": "File",
"checksum": "sha1$cb78aab1db8484d43ac0ae77b8da129e7e7049e4",
"size": 168,
"http://commonwl.org/cwltool#generation": 0
},
"resultvtu": {
"location": "file:///tmp/ktyym5s8/result000000.vtu",
"basename": "result000000.vtu",
"nameroot": "result000000",
"nameext": ".vtu",
"class": "File",
"checksum": "sha1$3e2e3c400d2efabbe2ba97051431a2275ef0074c",
"size": 8889,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step run_simulation] produced output {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#run_simulation/resultvtu": {
"location": "file:///tmp/ktyym5s8/result000000.vtu",
"basename": "result000000.vtu",
"nameroot": "result000000",
"nameext": ".vtu",
"class": "File",
"checksum": "sha1$3e2e3c400d2efabbe2ba97051431a2275ef0074c",
"size": 8889,
"http://commonwl.org/cwltool#generation": 0
},
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#run_simulation/resultpvd": {
"location": "file:///tmp/ktyym5s8/result.pvd",
"basename": "result.pvd",
"nameroot": "result",
"nameext": ".pvd",
"class": "File",
"checksum": "sha1$cb78aab1db8484d43ac0ae77b8da129e7e7049e4",
"size": 168,
"http://commonwl.org/cwltool#generation": 0
},
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#run_simulation/num_dofs": 357
}
INFO [step run_simulation] completed success
DEBUG [job run_simulation] Removing input staging directory /tmp/b744q5ut
DEBUG [job run_simulation] Removing temporary directory /tmp/upth1z9n
INFO [workflow ] starting step plot_over_line
DEBUG [step plot_over_line] job input {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#plot_over_line/pvdfile": {
"location": "file:///tmp/ktyym5s8/result.pvd",
"basename": "result.pvd",
"nameroot": "result",
"nameext": ".pvd",
"class": "File",
"checksum": "sha1$cb78aab1db8484d43ac0ae77b8da129e7e7049e4",
"size": 168,
"http://commonwl.org/cwltool#generation": 0
},
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#plot_over_line/vtkfile": {
"location": "file:///tmp/ktyym5s8/result000000.vtu",
"basename": "result000000.vtu",
"nameroot": "result000000",
"nameext": ".vtu",
"class": "File",
"checksum": "sha1$3e2e3c400d2efabbe2ba97051431a2275ef0074c",
"size": 8889,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step plot_over_line] evaluated job input to {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#plot_over_line/pvdfile": {
"location": "file:///tmp/ktyym5s8/result.pvd",
"basename": "result.pvd",
"nameroot": "result",
"nameext": ".pvd",
"class": "File",
"checksum": "sha1$cb78aab1db8484d43ac0ae77b8da129e7e7049e4",
"size": 168,
"http://commonwl.org/cwltool#generation": 0
},
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#plot_over_line/vtkfile": {
"location": "file:///tmp/ktyym5s8/result000000.vtu",
"basename": "result000000.vtu",
"nameroot": "result000000",
"nameext": ".vtu",
"class": "File",
"checksum": "sha1$3e2e3c400d2efabbe2ba97051431a2275ef0074c",
"size": 8889,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step plot_over_line] start
DEBUG [job plot_over_line] initializing from file:///tmp/simple_use_case/cwl/make_paraview_plot.cwl as part of step plot_over_line
DEBUG [job plot_over_line] {
"pvdfile": {
"location": "file:///tmp/ktyym5s8/result.pvd",
"basename": "result.pvd",
"nameroot": "result",
"nameext": ".pvd",
"class": "File",
"checksum": "sha1$cb78aab1db8484d43ac0ae77b8da129e7e7049e4",
"size": 168,
"http://commonwl.org/cwltool#generation": 0
},
"vtkfile": {
"location": "file:///tmp/ktyym5s8/result000000.vtu",
"basename": "result000000.vtu",
"nameroot": "result000000",
"nameext": ".vtu",
"class": "File",
"checksum": "sha1$3e2e3c400d2efabbe2ba97051431a2275ef0074c",
"size": 8889,
"http://commonwl.org/cwltool#generation": 0
},
"script": {
"class": "File",
"location": "file:///tmp/simple_use_case/source/postprocessing.py",
"basename": "postprocessing.py",
"nameroot": "postprocessing",
"nameext": ".py",
"size": 1479
}
}
DEBUG [job plot_over_line] path mappings is {
"file:///tmp/ktyym5s8/result.pvd": [
"/tmp/ktyym5s8/result.pvd",
"/tmp/q4we4jat/result.pvd",
"File",
false
],
"file:///tmp/simple_use_case/source/postprocessing.py": [
"/tmp/simple_use_case/source/postprocessing.py",
"/tmp/_wt9u6ok/stg3f246a31-4ab1-4b1e-9e76-cac36ba884e3/postprocessing.py",
"File",
true
],
"file:///tmp/ktyym5s8/result000000.vtu": [
"/tmp/ktyym5s8/result000000.vtu",
"/tmp/q4we4jat/result000000.vtu",
"File",
false
]
}
DEBUG [job plot_over_line] command line bindings is [
{
"position": [
-1000000,
0
],
"datum": "pvbatch"
},
{
"position": [
0,
0
],
"valueFrom": "$(inputs.script)"
},
{
"position": [
0,
1
],
"valueFrom": "$(inputs.pvdfile.path)"
},
{
"position": [
0,
2
],
"datum": "plotoverline.csv"
}
]
DEBUG [job plot_over_line] initial work dir {
"file:///tmp/ktyym5s8/result000000.vtu": [
"/tmp/ktyym5s8/result000000.vtu",
"/tmp/q4we4jat/result000000.vtu",
"File",
true
],
"file:///tmp/ktyym5s8/result.pvd": [
"/tmp/ktyym5s8/result.pvd",
"/tmp/q4we4jat/result.pvd",
"File",
true
]
}
INFO [job plot_over_line] /tmp/q4we4jat$ pvbatch \
/tmp/_wt9u6ok/stg3f246a31-4ab1-4b1e-9e76-cac36ba884e3/postprocessing.py \
/tmp/q4we4jat/result.pvd \
plotoverline.csv
Collecting package metadata: ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/simple_use_case/cwl/cwltool_deps/_conda/envs/[email protected]=hfc1cbd4_3_egl
added / updated specs:
- paraview==5.9.1=hfc1cbd4_3_egl
The following packages will be downloaded:
package | build
---------------------------|-----------------
appdirs-1.4.4 | pyh9f0ad1d_0 13 KB conda-forge
attrs-21.4.0 | pyhd8ed1ab_0 49 KB conda-forge
automat-20.2.0 | py_0 30 KB conda-forge
bcrypt-3.2.2 | py39hb9d737c_0 44 KB conda-forge
brotli-1.0.9 | h166bdaf_7 18 KB conda-forge
brotli-bin-1.0.9 | h166bdaf_7 19 KB conda-forge
certifi-2021.10.8 | py39hf3d152e_2 145 KB conda-forge
cffi-1.15.0 | py39h4bc2ebd_0 227 KB conda-forge
cgns-4.2.0 | h3c40bf4_2 851 KB conda-forge
constantly-15.1.0 | py_0 9 KB conda-forge
cryptography-36.0.2 | py39hd97740a_1 1.6 MB conda-forge
curl-7.83.0 | h7bff187_0 89 KB conda-forge
cycler-0.11.0 | pyhd8ed1ab_0 10 KB conda-forge
double-conversion-3.1.7 | h9c3ff4c_0 86 KB conda-forge
fonttools-4.33.3 | py39hb9d737c_0 1.6 MB conda-forge
giflib-5.2.1 | h36c2ea0_2 77 KB conda-forge
gl2ps-1.4.2 | h0708190_0 147 KB conda-forge
hdf5-1.10.6 |nompi_h6a2412b_1114 3.1 MB conda-forge
hyperlink-21.0.0 | pyhd3deb0d_0 71 KB conda-forge
idna-3.3 | pyhd8ed1ab_0 55 KB conda-forge
incremental-21.3.0 | pyhd8ed1ab_0 16 KB conda-forge
jbig-2.1 | h7f98852_2003 43 KB conda-forge
jsoncpp-1.9.4 | h4bd325d_3 262 KB conda-forge
kiwisolver-1.4.2 | py39hf939315_1 75 KB conda-forge
lcms2-2.12 | hddcbb42_0 443 KB conda-forge
lerc-3.0 | h9c3ff4c_0 216 KB conda-forge
libbrotlicommon-1.0.9 | h166bdaf_7 65 KB conda-forge
libbrotlidec-1.0.9 | h166bdaf_7 33 KB conda-forge
libbrotlienc-1.0.9 | h166bdaf_7 287 KB conda-forge
libdeflate-1.10 | h7f98852_0 77 KB conda-forge
libiconv-1.16 | h516909a_0 1.4 MB conda-forge
libnetcdf-4.8.1 |nompi_hcd642e3_100 1.4 MB conda-forge
libogg-1.3.4 | h7f98852_1 206 KB conda-forge
libprotobuf-3.18.1 | h780b84a_0 2.6 MB conda-forge
libtheora-1.1.1 | h7f98852_1005 651 KB conda-forge
libtiff-4.3.0 | h542a066_3 638 KB conda-forge
libvorbis-1.3.7 | h9c3ff4c_0 280 KB conda-forge
libwebp-1.2.2 | h3452ae3_0 85 KB conda-forge
libwebp-base-1.2.2 | h7f98852_1 824 KB conda-forge
libxml2-2.9.14 | h22db469_0 770 KB conda-forge
libzip-1.8.0 | h4de3113_1 126 KB conda-forge
matplotlib-base-3.5.1 | py39h2fa2bec_0 7.4 MB conda-forge
munkres-1.1.4 | pyh9f0ad1d_0 12 KB conda-forge
openjpeg-2.4.0 | hb52868f_1 444 KB conda-forge
packaging-21.3 | pyhd8ed1ab_0 36 KB conda-forge
paraview-5.9.1 | hfc1cbd4_3_egl 66.0 MB conda-forge
pillow-9.1.0 | py39hae2aec6_2 45.0 MB conda-forge
pugixml-1.11.4 | h9c3ff4c_0 125 KB conda-forge
pyasn1-0.4.8 | py_0 53 KB conda-forge
pyasn1-modules-0.2.7 | py_0 60 KB conda-forge
pycparser-2.21 | pyhd8ed1ab_0 100 KB conda-forge
pyopenssl-22.0.0 | pyhd8ed1ab_0 49 KB conda-forge
pyparsing-3.0.8 | pyhd8ed1ab_0 79 KB conda-forge
python-dateutil-2.8.2 | pyhd8ed1ab_0 240 KB conda-forge
service_identity-18.1.0 | py_0 12 KB conda-forge
twisted-22.4.0 | py39hb9d737c_0 5.1 MB conda-forge
typing-extensions-4.2.0 | hd8ed1ab_1 8 KB conda-forge
typing_extensions-4.2.0 | pyha770c72_1 27 KB conda-forge
unicodedata2-14.0.0 | py39hb9d737c_1 498 KB conda-forge
zope.interface-5.4.0 | py39hb9d737c_2 323 KB conda-forge
------------------------------------------------------------
Total: 144.0 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
appdirs conda-forge/noarch::appdirs-1.4.4-pyh9f0ad1d_0
attrs conda-forge/noarch::attrs-21.4.0-pyhd8ed1ab_0
automat conda-forge/noarch::automat-20.2.0-py_0
bcrypt conda-forge/linux-64::bcrypt-3.2.2-py39hb9d737c_0
brotli conda-forge/linux-64::brotli-1.0.9-h166bdaf_7
brotli-bin conda-forge/linux-64::brotli-bin-1.0.9-h166bdaf_7
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
c-ares conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
ca-certificates conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
certifi conda-forge/linux-64::certifi-2021.10.8-py39hf3d152e_2
cffi conda-forge/linux-64::cffi-1.15.0-py39h4bc2ebd_0
cgns conda-forge/linux-64::cgns-4.2.0-h3c40bf4_2
constantly conda-forge/noarch::constantly-15.1.0-py_0
cryptography conda-forge/linux-64::cryptography-36.0.2-py39hd97740a_1
curl conda-forge/linux-64::curl-7.83.0-h7bff187_0
cycler conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
double-conversion conda-forge/linux-64::double-conversion-3.1.7-h9c3ff4c_0
expat conda-forge/linux-64::expat-2.4.8-h27087fc_0
fonttools conda-forge/linux-64::fonttools-4.33.3-py39hb9d737c_0
freetype conda-forge/linux-64::freetype-2.10.4-h0708190_1
giflib conda-forge/linux-64::giflib-5.2.1-h36c2ea0_2
gl2ps conda-forge/linux-64::gl2ps-1.4.2-h0708190_0
hdf4 conda-forge/linux-64::hdf4-4.2.15-h10796ff_3
hdf5 conda-forge/linux-64::hdf5-1.10.6-nompi_h6a2412b_1114
hyperlink conda-forge/noarch::hyperlink-21.0.0-pyhd3deb0d_0
icu conda-forge/linux-64::icu-70.1-h27087fc_0
idna conda-forge/noarch::idna-3.3-pyhd8ed1ab_0
incremental conda-forge/noarch::incremental-21.3.0-pyhd8ed1ab_0
jbig conda-forge/linux-64::jbig-2.1-h7f98852_2003
jpeg conda-forge/linux-64::jpeg-9e-h166bdaf_1
jsoncpp conda-forge/linux-64::jsoncpp-1.9.4-h4bd325d_3
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
kiwisolver conda-forge/linux-64::kiwisolver-1.4.2-py39hf939315_1
krb5 conda-forge/linux-64::krb5-1.19.3-h3790be6_0
lcms2 conda-forge/linux-64::lcms2-2.12-hddcbb42_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
lerc conda-forge/linux-64::lerc-3.0-h9c3ff4c_0
libblas conda-forge/linux-64::libblas-3.9.0-14_linux64_openblas
libbrotlicommon conda-forge/linux-64::libbrotlicommon-1.0.9-h166bdaf_7
libbrotlidec conda-forge/linux-64::libbrotlidec-1.0.9-h166bdaf_7
libbrotlienc conda-forge/linux-64::libbrotlienc-1.0.9-h166bdaf_7
libcblas conda-forge/linux-64::libcblas-3.9.0-14_linux64_openblas
libcurl conda-forge/linux-64::libcurl-7.83.0-h7bff187_0
libdeflate conda-forge/linux-64::libdeflate-1.10-h7f98852_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_16
libgfortran-ng conda-forge/linux-64::libgfortran-ng-11.2.0-h69a702a_16
libgfortran5 conda-forge/linux-64::libgfortran5-11.2.0-h5c6108e_16
libgomp conda-forge/linux-64::libgomp-11.2.0-h1d223b6_16
libiconv conda-forge/linux-64::libiconv-1.16-h516909a_0
liblapack conda-forge/linux-64::liblapack-3.9.0-14_linux64_openblas
libnetcdf conda-forge/linux-64::libnetcdf-4.8.1-nompi_hcd642e3_100
libnghttp2 conda-forge/linux-64::libnghttp2-1.47.0-h727a467_0
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libogg conda-forge/linux-64::libogg-1.3.4-h7f98852_1
libopenblas conda-forge/linux-64::libopenblas-0.3.20-pthreads_h78a6416_0
libpng conda-forge/linux-64::libpng-1.6.37-h21135ba_2
libprotobuf conda-forge/linux-64::libprotobuf-3.18.1-h780b84a_0
libssh2 conda-forge/linux-64::libssh2-1.10.0-ha56f1ee_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_16
libtheora conda-forge/linux-64::libtheora-1.1.1-h7f98852_1005
libtiff conda-forge/linux-64::libtiff-4.3.0-h542a066_3
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libvorbis conda-forge/linux-64::libvorbis-1.3.7-h9c3ff4c_0
libwebp conda-forge/linux-64::libwebp-1.2.2-h3452ae3_0
libwebp-base conda-forge/linux-64::libwebp-base-1.2.2-h7f98852_1
libxcb conda-forge/linux-64::libxcb-1.13-h7f98852_1004
libxml2 conda-forge/linux-64::libxml2-2.9.14-h22db469_0
libzip conda-forge/linux-64::libzip-1.8.0-h4de3113_1
libzlib conda-forge/linux-64::libzlib-1.2.11-h166bdaf_1014
lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_1
matplotlib-base conda-forge/linux-64::matplotlib-base-3.5.1-py39h2fa2bec_0
munkres conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
numpy conda-forge/linux-64::numpy-1.22.3-py39hc58783e_2
openjpeg conda-forge/linux-64::openjpeg-2.4.0-hb52868f_1
openssl conda-forge/linux-64::openssl-1.1.1n-h166bdaf_0
packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
paraview conda-forge/linux-64::paraview-5.9.1-hfc1cbd4_3_egl
pillow conda-forge/linux-64::pillow-9.1.0-py39hae2aec6_2
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
pugixml conda-forge/linux-64::pugixml-1.11.4-h9c3ff4c_0
pyasn1 conda-forge/noarch::pyasn1-0.4.8-py_0
pyasn1-modules conda-forge/noarch::pyasn1-modules-0.2.7-py_0
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
pyopenssl conda-forge/noarch::pyopenssl-22.0.0-pyhd8ed1ab_0
pyparsing conda-forge/noarch::pyparsing-3.0.8-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.9.12-h9a8a25e_1_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.9-2_cp39
readline conda-forge/linux-64::readline-8.1-h46c0cb4_0
service_identity conda-forge/noarch::service_identity-18.1.0-py_0
setuptools conda-forge/linux-64::setuptools-62.1.0-py39hf3d152e_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
sqlite conda-forge/linux-64::sqlite-3.38.3-h4ff8645_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
twisted conda-forge/linux-64::twisted-22.4.0-py39hb9d737c_0
typing-extensions conda-forge/noarch::typing-extensions-4.2.0-hd8ed1ab_1
typing_extensions conda-forge/noarch::typing_extensions-4.2.0-pyha770c72_1
tzdata conda-forge/noarch::tzdata-2022a-h191b570_0
unicodedata2 conda-forge/linux-64::unicodedata2-14.0.0-py39hb9d737c_1
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
zlib conda-forge/linux-64::zlib-1.2.11-h166bdaf_1014
zope.interface conda-forge/linux-64::zope.interface-5.4.0-py39hb9d737c_2
zstd conda-forge/linux-64::zstd-1.5.2-ha95c52a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
/tmp/simple_use_case/cwl/cwltool_deps/_conda/lib/python3.7/site-packages/cryptography/hazmat/backends/openssl/x509.py:17: CryptographyDeprecationWarning: This version of cryptography contains a temporary pyOpenSSL fallback path. Upgrade pyOpenSSL now.
utils.DeprecatedIn35,
INFO [job plot_over_line] completed success
DEBUG [job plot_over_line] outputs {
"resultcsv": {
"location": "file:///tmp/q4we4jat/plotoverline.csv",
"basename": "plotoverline.csv",
"nameroot": "plotoverline",
"nameext": ".csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step plot_over_line] produced output {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#plot_over_line/resultcsv": {
"location": "file:///tmp/q4we4jat/plotoverline.csv",
"basename": "plotoverline.csv",
"nameroot": "plotoverline",
"nameext": ".csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step plot_over_line] completed success
DEBUG [job plot_over_line] Removing input staging directory /tmp/_wt9u6ok
DEBUG [job plot_over_line] Removing temporary directory /tmp/8tcfpyv0
INFO [workflow ] starting step prepare_paper_macros
DEBUG [step prepare_paper_macros] job input {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#prepare_paper_macros/domain_size": 1.0,
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#prepare_paper_macros/num_dofs": 357,
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#prepare_paper_macros/plot_data_file": {
"location": "file:///tmp/q4we4jat/plotoverline.csv",
"basename": "plotoverline.csv",
"nameroot": "plotoverline",
"nameext": ".csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step prepare_paper_macros] evaluated job input to {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#prepare_paper_macros/domain_size": 1.0,
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#prepare_paper_macros/num_dofs": 357,
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#prepare_paper_macros/plot_data_file": {
"location": "file:///tmp/q4we4jat/plotoverline.csv",
"basename": "plotoverline.csv",
"nameroot": "plotoverline",
"nameext": ".csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step prepare_paper_macros] start
DEBUG [job prepare_paper_macros] initializing from file:///tmp/simple_use_case/cwl/prepare_paper_macros.cwl as part of step prepare_paper_macros
DEBUG [job prepare_paper_macros] {
"domain_size": 1.0,
"num_dofs": 357,
"plot_data_file": {
"location": "file:///tmp/q4we4jat/plotoverline.csv",
"basename": "plotoverline.csv",
"nameroot": "plotoverline",
"nameext": ".csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"http://commonwl.org/cwltool#generation": 0
},
"macros_template": {
"class": "File",
"location": "file:///tmp/simple_use_case/source/macros.tex.template",
"basename": "macros.tex.template",
"nameroot": "macros.tex",
"nameext": ".template",
"size": 118
},
"substitution_script": {
"class": "File",
"location": "file:///tmp/simple_use_case/source/prepare_paper_macros.py",
"basename": "prepare_paper_macros.py",
"nameroot": "prepare_paper_macros",
"nameext": ".py",
"size": 1209
}
}
DEBUG [job prepare_paper_macros] path mappings is {
"file:///tmp/simple_use_case/source/macros.tex.template": [
"/tmp/simple_use_case/source/macros.tex.template",
"/tmp/rd45rkce/macros.tex.template",
"File",
false
],
"file:///tmp/q4we4jat/plotoverline.csv": [
"/tmp/q4we4jat/plotoverline.csv",
"/tmp/uq2tvqrs/stg69cec46e-9cec-4a10-99b1-f1ac70804b28/plotoverline.csv",
"File",
true
],
"file:///tmp/simple_use_case/source/prepare_paper_macros.py": [
"/tmp/simple_use_case/source/prepare_paper_macros.py",
"/tmp/rd45rkce/prepare_paper_macros.py",
"File",
false
]
}
DEBUG [job prepare_paper_macros] command line bindings is [
{
"position": [
-1000000,
0
],
"datum": "python3"
},
{
"position": [
0,
0
],
"valueFrom": "$(inputs.substitution_script)"
},
{
"position": [
0,
1
],
"datum": "--domain-size"
},
{
"position": [
0,
2
],
"valueFrom": "$(inputs.domain_size)"
},
{
"position": [
0,
3
],
"datum": "--macro-template-file"
},
{
"position": [
0,
4
],
"valueFrom": "$(inputs.macros_template)"
},
{
"position": [
0,
5
],
"datum": "--output-macro-file"
},
{
"position": [
0,
6
],
"datum": "macros.tex"
},
{
"position": [
0,
7
],
"datum": "--num-dofs"
},
{
"position": [
0,
8
],
"valueFrom": "$(inputs.num_dofs)"
},
{
"position": [
0,
9
],
"datum": "--plot-data-path"
},
{
"position": [
0,
10
],
"valueFrom": "$(inputs.plot_data_file.basename)"
}
]
DEBUG [job prepare_paper_macros] initial work dir {
"file:///tmp/simple_use_case/source/prepare_paper_macros.py": [
"/tmp/simple_use_case/source/prepare_paper_macros.py",
"/tmp/rd45rkce/prepare_paper_macros.py",
"File",
true
],
"file:///tmp/simple_use_case/source/macros.tex.template": [
"/tmp/simple_use_case/source/macros.tex.template",
"/tmp/rd45rkce/macros.tex.template",
"File",
true
]
}
INFO [job prepare_paper_macros] /tmp/rd45rkce$ python3 \
/tmp/rd45rkce/prepare_paper_macros.py \
--domain-size \
1.0 \
--macro-template-file \
/tmp/rd45rkce/macros.tex.template \
--output-macro-file \
macros.tex \
--num-dofs \
357 \
--plot-data-path \
plotoverline.csv
INFO [job prepare_paper_macros] completed success
DEBUG [job prepare_paper_macros] outputs {
"macros_file": {
"location": "file:///tmp/rd45rkce/macros.tex",
"basename": "macros.tex",
"nameroot": "macros",
"nameext": ".tex",
"class": "File",
"checksum": "sha1$7e3a524912967f8f7a25ebca68aafddbe13677d8",
"size": 102,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step prepare_paper_macros] produced output {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#prepare_paper_macros/macros_file": {
"location": "file:///tmp/rd45rkce/macros.tex",
"basename": "macros.tex",
"nameroot": "macros",
"nameext": ".tex",
"class": "File",
"checksum": "sha1$7e3a524912967f8f7a25ebca68aafddbe13677d8",
"size": 102,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step prepare_paper_macros] completed success
DEBUG [job prepare_paper_macros] Removing input staging directory /tmp/uq2tvqrs
DEBUG [job prepare_paper_macros] Removing temporary directory /tmp/bca4efbe
INFO [workflow ] starting step compile_paper
DEBUG [step compile_paper] job input {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#compile_paper/csvfile": {
"location": "file:///tmp/q4we4jat/plotoverline.csv",
"basename": "plotoverline.csv",
"nameroot": "plotoverline",
"nameext": ".csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"http://commonwl.org/cwltool#generation": 0
},
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#compile_paper/macros": {
"location": "file:///tmp/rd45rkce/macros.tex",
"basename": "macros.tex",
"nameroot": "macros",
"nameext": ".tex",
"class": "File",
"checksum": "sha1$7e3a524912967f8f7a25ebca68aafddbe13677d8",
"size": 102,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step compile_paper] evaluated job input to {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#compile_paper/csvfile": {
"location": "file:///tmp/q4we4jat/plotoverline.csv",
"basename": "plotoverline.csv",
"nameroot": "plotoverline",
"nameext": ".csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"http://commonwl.org/cwltool#generation": 0
},
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#compile_paper/macros": {
"location": "file:///tmp/rd45rkce/macros.tex",
"basename": "macros.tex",
"nameroot": "macros",
"nameext": ".tex",
"class": "File",
"checksum": "sha1$7e3a524912967f8f7a25ebca68aafddbe13677d8",
"size": 102,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step compile_paper] start
DEBUG [job compile_paper] initializing from file:///tmp/simple_use_case/cwl/compile_paper.cwl as part of step compile_paper
DEBUG [job compile_paper] {
"csvfile": {
"location": "file:///tmp/q4we4jat/plotoverline.csv",
"basename": "plotoverline.csv",
"nameroot": "plotoverline",
"nameext": ".csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"http://commonwl.org/cwltool#generation": 0
},
"macros": {
"location": "file:///tmp/rd45rkce/macros.tex",
"basename": "macros.tex",
"nameroot": "macros",
"nameext": ".tex",
"class": "File",
"checksum": "sha1$7e3a524912967f8f7a25ebca68aafddbe13677d8",
"size": 102,
"http://commonwl.org/cwltool#generation": 0
},
"texfile": {
"class": "File",
"location": "file:///tmp/simple_use_case/source/paper.tex",
"basename": "paper.tex",
"nameroot": "paper",
"nameext": ".tex",
"size": 585
}
}
DEBUG [job compile_paper] path mappings is {
"file:///tmp/q4we4jat/plotoverline.csv": [
"/tmp/q4we4jat/plotoverline.csv",
"/tmp/8ox76kll/plotoverline.csv",
"File",
false
],
"file:///tmp/rd45rkce/macros.tex": [
"/tmp/rd45rkce/macros.tex",
"/tmp/8ox76kll/macros.tex",
"File",
false
],
"file:///tmp/simple_use_case/source/paper.tex": [
"/tmp/simple_use_case/source/paper.tex",
"/tmp/8ox76kll/paper.tex",
"File",
false
]
}
DEBUG [job compile_paper] command line bindings is [
{
"position": [
-1000000,
0
],
"datum": "tectonic"
},
{
"position": [
0,
0
],
"valueFrom": "$(inputs.texfile)"
}
]
DEBUG [job compile_paper] initial work dir {
"file:///tmp/q4we4jat/plotoverline.csv": [
"/tmp/q4we4jat/plotoverline.csv",
"/tmp/8ox76kll/plotoverline.csv",
"File",
true
],
"file:///tmp/simple_use_case/source/paper.tex": [
"/tmp/simple_use_case/source/paper.tex",
"/tmp/8ox76kll/paper.tex",
"File",
true
],
"file:///tmp/rd45rkce/macros.tex": [
"/tmp/rd45rkce/macros.tex",
"/tmp/8ox76kll/macros.tex",
"File",
true
]
}
INFO [job compile_paper] /tmp/8ox76kll$ tectonic \
/tmp/8ox76kll/paper.tex
Collecting package metadata: ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/simple_use_case/cwl/cwltool_deps/_conda/envs/[email protected]=ha1fef3e_1
added / updated specs:
- tectonic==0.8.0=ha1fef3e_1
The following packages will be downloaded:
package | build
---------------------------|-----------------
cairo-1.16.0 | h6cf1ce9_1008 1.5 MB conda-forge
font-ttf-dejavu-sans-mono-2.37| hab24e00_0 388 KB conda-forge
font-ttf-inconsolata-3.000 | h77eed37_0 94 KB conda-forge
font-ttf-source-code-pro-2.038| h77eed37_0 684 KB conda-forge
font-ttf-ubuntu-0.83 | hab24e00_0 1.9 MB conda-forge
fonts-conda-ecosystem-1 | 0 4 KB conda-forge
fonts-conda-forge-1 | 0 4 KB conda-forge
gettext-0.19.8.1 | h73d1719_1008 3.6 MB conda-forge
graphite2-1.3.13 | h58526e2_1001 102 KB conda-forge
harfbuzz-3.1.1 | h83ec7ef_0 2.1 MB conda-forge
icu-68.2 | h9c3ff4c_0 13.1 MB conda-forge
libglib-2.70.2 | h174f98d_4 3.1 MB conda-forge
pcre-8.45 | h9c3ff4c_0 253 KB conda-forge
pixman-0.40.0 | h36c2ea0_0 627 KB conda-forge
tectonic-0.8.0 | ha1fef3e_1 4.5 MB conda-forge
------------------------------------------------------------
Total: 31.9 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
cairo conda-forge/linux-64::cairo-1.16.0-h6cf1ce9_1008
expat conda-forge/linux-64::expat-2.4.8-h27087fc_0
font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0
font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0
font-ttf-ubuntu conda-forge/noarch::font-ttf-ubuntu-0.83-hab24e00_0
fontconfig conda-forge/linux-64::fontconfig-2.14.0-h8e229c2_0
fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0
fonts-conda-forge conda-forge/noarch::fonts-conda-forge-1-0
freetype conda-forge/linux-64::freetype-2.10.4-h0708190_1
gettext conda-forge/linux-64::gettext-0.19.8.1-h73d1719_1008
graphite2 conda-forge/linux-64::graphite2-1.3.13-h58526e2_1001
harfbuzz conda-forge/linux-64::harfbuzz-3.1.1-h83ec7ef_0
icu conda-forge/linux-64::icu-68.2-h9c3ff4c_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_16
libglib conda-forge/linux-64::libglib-2.70.2-h174f98d_4
libgomp conda-forge/linux-64::libgomp-11.2.0-h1d223b6_16
libiconv conda-forge/linux-64::libiconv-1.16-h516909a_0
libpng conda-forge/linux-64::libpng-1.6.37-h21135ba_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_16
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libxcb conda-forge/linux-64::libxcb-1.13-h7f98852_1004
libzlib conda-forge/linux-64::libzlib-1.2.11-h166bdaf_1014
openssl conda-forge/linux-64::openssl-1.1.1n-h166bdaf_0
pcre conda-forge/linux-64::pcre-8.45-h9c3ff4c_0
pixman conda-forge/linux-64::pixman-0.40.0-h36c2ea0_0
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
tectonic conda-forge/linux-64::tectonic-0.8.0-ha1fef3e_1
xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002
xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h7f98852_0
xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-hd9c2040_1000
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.7.2-h7f98852_0
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h7f98852_1
xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h7f98852_1003
xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002
xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h7f98852_1002
xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007
zlib conda-forge/linux-64::zlib-1.2.11-h166bdaf_1014
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
/tmp/simple_use_case/cwl/cwltool_deps/_conda/lib/python3.7/site-packages/cryptography/hazmat/backends/openssl/x509.py:17: CryptographyDeprecationWarning: This version of cryptography contains a temporary pyOpenSSL fallback path. Upgrade pyOpenSSL now.
utils.DeprecatedIn35,
note: connecting to https://relay.fullyjustified.net/default_bundle.tar
note: resolved to https://data1.fullyjustified.net/tlextras-2020.0r0.tar
note: downloading index https://data1.fullyjustified.net/tlextras-2020.0r0.tar.index.gz
note: downloading SHA256SUM
note: generating format "latex"
note: downloading tectonic-format-latex.tex
note: downloading xelatex.ini
note: downloading latex.ltx
note: downloading texsys.cfg
note: downloading fonttext.cfg
note: downloading fonttext.ltx
note: downloading omlenc.def
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note: downloading tulmr.fd
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note: downloading ts1lmr.fd
note: downloading t1cmr.fd
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note: downloading fontmath.cfg
note: downloading fontmath.ltx
note: downloading omlcmm.fd
note: downloading omscmsy.fd
note: downloading omxcmex.fd
note: downloading ucmr.fd
note: downloading preload.cfg
note: downloading preload.ltx
note: downloading cmex10.tfm
note: downloading line10.tfm
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note: downloading cmr5.tfm
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note: downloading cmmi5.tfm
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note: downloading cmmi10.tfm
note: downloading cmsy5.tfm
note: downloading cmsy7.tfm
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note: downloading load-unicode-data.tex
note: downloading UnicodeData.txt
note: downloading hyphen.cfg
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note: downloading language.dat
note: downloading hyphen.tex
note: downloading dumyhyph.tex
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note: downloading dehypht-x-2019-04-04.tex
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note: Writing `/tmp/8ox76kll/paper.pdf` (39.02 KiB)
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INFO [job compile_paper] completed success
DEBUG [job compile_paper] outputs {
"pdf": {
"location": "file:///tmp/8ox76kll/paper.pdf",
"basename": "paper.pdf",
"nameroot": "paper",
"nameext": ".pdf",
"class": "File",
"checksum": "sha1$52b2aea30aa77775c2dd5bc5a538b24d9e89d09b",
"size": 39952,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [step compile_paper] produced output {
"file:///tmp/simple_use_case/cwl/wf_run_use_case.cwl#compile_paper/pdf": {
"location": "file:///tmp/8ox76kll/paper.pdf",
"basename": "paper.pdf",
"nameroot": "paper",
"nameext": ".pdf",
"class": "File",
"checksum": "sha1$52b2aea30aa77775c2dd5bc5a538b24d9e89d09b",
"size": 39952,
"http://commonwl.org/cwltool#generation": 0
}
}
INFO [step compile_paper] completed success
INFO [workflow ] completed success
DEBUG [workflow ] outputs {
"macros": {
"location": "file:///tmp/rd45rkce/macros.tex",
"basename": "macros.tex",
"nameroot": "macros",
"nameext": ".tex",
"class": "File",
"checksum": "sha1$7e3a524912967f8f7a25ebca68aafddbe13677d8",
"size": 102,
"http://commonwl.org/cwltool#generation": 0
},
"paperpdf": {
"location": "file:///tmp/8ox76kll/paper.pdf",
"basename": "paper.pdf",
"nameroot": "paper",
"nameext": ".pdf",
"class": "File",
"checksum": "sha1$52b2aea30aa77775c2dd5bc5a538b24d9e89d09b",
"size": 39952,
"http://commonwl.org/cwltool#generation": 0
},
"pol_data": {
"location": "file:///tmp/q4we4jat/plotoverline.csv",
"basename": "plotoverline.csv",
"nameroot": "plotoverline",
"nameext": ".csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"http://commonwl.org/cwltool#generation": 0
},
"resultvtu": {
"location": "file:///tmp/ktyym5s8/result000000.vtu",
"basename": "result000000.vtu",
"nameroot": "result000000",
"nameext": ".vtu",
"class": "File",
"checksum": "sha1$3e2e3c400d2efabbe2ba97051431a2275ef0074c",
"size": 8889,
"http://commonwl.org/cwltool#generation": 0
}
}
DEBUG [job compile_paper] Removing input staging directory /tmp/w2w9rcha
DEBUG [job compile_paper] Removing temporary directory /tmp/rel8326u
DEBUG Moving /tmp/rd45rkce/macros.tex to /tmp/simple_use_case/cwl/macros.tex
DEBUG Moving /tmp/8ox76kll/paper.pdf to /tmp/simple_use_case/cwl/paper.pdf
DEBUG Moving /tmp/q4we4jat/plotoverline.csv to /tmp/simple_use_case/cwl/plotoverline.csv
DEBUG Moving /tmp/ktyym5s8/result000000.vtu to /tmp/simple_use_case/cwl/result000000.vtu
DEBUG Removing intermediate output directory /tmp/znbl37qp
DEBUG Removing intermediate output directory /tmp/rd45rkce
DEBUG Removing intermediate output directory /tmp/q4we4jat
DEBUG Removing intermediate output directory /tmp/porwxmx7
DEBUG Removing intermediate output directory /tmp/ktyym5s8
DEBUG Removing intermediate output directory /tmp/6d5f4j4s
DEBUG Removing intermediate output directory /tmp/8ox76kll
{
"macros": {
"location": "file:///tmp/simple_use_case/cwl/macros.tex",
"basename": "macros.tex",
"class": "File",
"checksum": "sha1$7e3a524912967f8f7a25ebca68aafddbe13677d8",
"size": 102,
"path": "/tmp/simple_use_case/cwl/macros.tex"
},
"paperpdf": {
"location": "file:///tmp/simple_use_case/cwl/paper.pdf",
"basename": "paper.pdf",
"class": "File",
"checksum": "sha1$52b2aea30aa77775c2dd5bc5a538b24d9e89d09b",
"size": 39952,
"path": "/tmp/simple_use_case/cwl/paper.pdf"
},
"pol_data": {
"location": "file:///tmp/simple_use_case/cwl/plotoverline.csv",
"basename": "plotoverline.csv",
"class": "File",
"checksum": "sha1$63390a713a3103836091df32a6d90e0532440620",
"size": 30412,
"path": "/tmp/simple_use_case/cwl/plotoverline.csv"
},
"resultvtu": {
"location": "file:///tmp/simple_use_case/cwl/result000000.vtu",
"basename": "result000000.vtu",
"class": "File",
"checksum": "sha1$3e2e3c400d2efabbe2ba97051431a2275ef0074c",
"size": 8889,
"path": "/tmp/simple_use_case/cwl/result000000.vtu"
}
}
INFO Final process status is success

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