run_d3d_parallel.sh

#!/bin/bash
#$ -V
#$ -j yes

set NHOSTS manually here:
export NHOSTS=2
NPART=$NHOSTS
#
# This script starts a single-domain Delft3D-FLOW computation on Linux in parallel mode
# asuming nodes are allocated manually
#
# Usage example:
# Create a file named machinefile as described below
# Execute this script
#
# In case the error "unable to find mpd.conf" occurs:
# Your home directory MUST contain file .mpd.conf with contents:
# secretword=bla
# and with file access permissions:
# -r--------
# 


#
# Specify the config file to be used here
# 
argfile=config.xml

#
# Set the directory containing delftflow.exe here
#
export ARCH=lnx
export D3D_HOME=delft3d/bin
exedir=$D3D_HOME/$ARCH/flow2d3d/bin
 
#
# No adaptions needed below
#

# Set some (environment) parameters
export LD_LIBRARY_PATH=$exedir:$LD_LIBRARY_PATH 



### Specific setting for H3/H4 linuxclusters, needed for MPICH2
### commands (mpdboot, mpirun, mpiexed, mpdallexit etc.).
export PATH="/opt/mpich2/bin:${PATH}"
 
### The file "machinefile" is assumed to be created manually and should
### look like:
### machinename1:2
### machinename2:2
### machinename3:2

echo Contents of machinefile:
cat $(pwd)/machinefile
echo ----------------------------------------------------------------------

# Run

### command="d3d.run -nproc "$NHOSTS" -input "$inputfile" -back no
### eval $command

### General for MPICH2, startup your MPICH2 communication network (you
### can check if it is already there with mpdtrace).
###
### The use of hydra instead of mpd is adviced. hydra is the default for mpich2 version 1.4.1
### From the README:
### hydra
### -----
### Hydra is the default process management framework that uses existing 
### daemons on nodes (e.g., ssh, pbs, slurm, sge) to start MPI processes. 
### More information on Hydra can be found at 
### http://wiki.mcs.anl.gov/mpich2/index.php/Using_the_Hydra_Process_Manager
### 
### mpd
### ---
### MPD was the traditional process manager in MPICH2. The file 
### mpich2-1.4.1/src/pm/mpd/README has more information about interactive commands 
### for managing the ring of MPDs. The MPD process manager is now deprecated.
mpd &


### Optionally:
### Add option --rsh=/usr/bin/rsh to mpdboot
### This is needed when the following error appears:
### mpdboot_xh5000 (handle_mpd_output 420): from mpd on xh5001, invalid port info: no_port
mpdboot -n $NHOSTS -f $(pwd)/machinefile --ncpus=2

# link mpich debug rubbish to /dev/null
node_number=$NPART
while test $node_number -ge 1
do
   node_number=`expr $node_number - 1`
   ln -s /dev/null log$node_number.irlog
done

### For debug purpose:
echo " "
echo "ldd libflow2d3d.so: start"
ldd $exedir/libflow2d3d.so
echo "ldd libflow2d3d.so: end"
echo " "

### General, start delftflow in parallel by means of mpirun.
### The machines in the h4 cluster are dual core; start 2*NHOSTS parallel processes
mpirun -np $NHOSTS $exedir/d_hydro.exe $argfile
### alternatives:
### mpiexec -n $DELTAQ_NumNodes delftflow_91.exe -r $inputfile.mdf
### mpiexec -n `expr $DELTAQ_NumNodes \* 2` $exedir/deltares_hydro.exe $argfile


rm -f log*.irlog

### General for MPICH2, finish your MPICH2 communication network.
mpdallexit 

Funny that this script gets some attention after 9 years. It’s a long time ago. I kept my shell script skills up to date the last years but never worked with delft3d since.

Can you share more details and the error? Maybe I can help.

Hi Martijn, Thank you so much for the response. I’m quite new in running the coupled simulations (WAVE+FLOW) via a cluster. I can’t remember the original error I had. Just to give you a little bit of background, I am using the scripts below: - run_dflow2d3d_parallel_dwaves.sh - and tnpa_cc_trial2.pbs (where I execute .sh) to try and run the coupled simulation. I am not sure how to set up the environment (which is included in the.pbs script), and I would appreciate your assistance. In addition, there is no literature or information on this topic. Does the.pbs script make sense? Specifically, where I run the model? I would appreciate it if you could share any information you have about this. Looking forward to hearing from you. Kind regards, Bafana

…

On Wed, 17 Apr 2024 at 21:40, Martijn Gastkemper ***@***.***> wrote: ***@***.**** commented on this gist. ------------------------------ Funny that this script gets some attention after 9 years. It’s a long time ago. I kept my shell script skills up to date the last years but never worked with delft3d since. Can you share more details and the error? Maybe I can help. — Reply to this email directly, view it on GitHub <https://gist.github.com/martijngastkemper/7dfce82d7e39869c725d#gistcomment-5027357> or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASXMSL4QTDDNQLMOOMAZ2W3Y53F2ZBFKMF2HI4TJMJ2XIZLTSKBKK5TBNR2WLJDUOJ2WLJDOMFWWLO3UNBZGKYLEL5YGC4TUNFRWS4DBNZ2F6YLDORUXM2LUPGBKK5TBNR2WLJDHNFZXJJDOMFWWLK3UNBZGKYLEL52HS4DFVRZXKYTKMVRXIX3UPFYGLK2HNFZXIQ3PNVWWK3TUUZ2G64DJMNZZDAVEOR4XAZNEM5UXG5FFOZQWY5LFVAYTQNRXGYYTGN5HORZGSZ3HMVZKMY3SMVQXIZI> . You are receiving this email because you commented on the thread. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub> .

I'm sorry but that beyond my knowledge.