Created
November 4, 2016 00:22
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| hayashis@h1(karst):/N/dc2/scratch/hayashis/tmp/python36 $ ./run.sh | |
| enabling debugging | |
| ending argument loop | |
| Exec'ing: /N/soft/rhel6/singularity/2.2/libexec/singularity/cli/exec.exec /N/u/hayashis/Karst/download/python_3.6-2016-11-01-156ca2b5b15f.imgVERBOSE [U=740536,P=13639] message.c:52:init() : Set messagelevel to: 5 | |
| DEBUG [U=740536,P=13639] privilege.c:66:singularity_priv_init() : Called singularity_priv_init(void) | |
| DEBUG [U=740536,P=13639] privilege.c:131:singularity_priv_init() : Returning singularity_priv_init(void) | |
| DEBUG [U=740536,P=13639] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13639] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| VERBOSE [U=740536,P=13639] sexec.c:73:main() : Running NON-SUID program workflow | |
| DEBUG [U=740536,P=13639] sexec.c:75:main() : Checking program has appropriate permissions | |
| VERBOSE [U=740536,P=13639] config_parser.c:43:singularity_config_open(): Opening configuration file: /N/soft/rhel6/singularity/2.2/etc/singularity/singularity.conf | |
| DEBUG [U=740536,P=13639] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| VERBOSE [U=740536,P=13639] sexec.c:85:main() : Checking that we are allowed to run as SUID | |
| DEBUG [U=740536,P=13639] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(allow setuid, 1) | |
| DEBUG [U=740536,P=13639] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(allow setuid) | |
| VERBOSE [U=740536,P=13639] config_parser.c:91:singularity_config_get_value(): Got config key allow setuid (= 'yes') | |
| DEBUG [U=740536,P=13639] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(allow setuid, 1) = 1 | |
| VERBOSE [U=740536,P=13639] sexec.c:87:main() : Checking if we were requested to run as NOSUID by user | |
| DEBUG [U=740536,P=13639] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_NOSUID | |
| VERBOSE [U=740536,P=13639] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_NOSUID | |
| VERBOSE [U=740536,P=13639] sexec.c:92:main() : Invoking SUID sexec: /N/soft/rhel6/singularity/2.2/libexec/singularity/sexec-suid | |
| VERBOSE [U=0,P=13639] message.c:52:init() : Set messagelevel to: 5 | |
| DEBUG [U=0,P=13639] privilege.c:66:singularity_priv_init() : Called singularity_priv_init(void) | |
| DEBUG [U=0,P=13639] privilege.c:131:singularity_priv_init() : Returning singularity_priv_init(void) | |
| DEBUG [U=0,P=13639] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13639] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| VERBOSE [U=740536,P=13639] sexec.c:46:main() : Running SUID program workflow | |
| VERBOSE [U=740536,P=13639] sexec.c:48:main() : Checking program has appropriate permissions | |
| VERBOSE [U=740536,P=13639] sexec.c:53:main() : Checking configuration file is properly owned by root | |
| VERBOSE [U=740536,P=13639] config_parser.c:43:singularity_config_open(): Opening configuration file: /N/soft/rhel6/singularity/2.2/etc/singularity/singularity.conf | |
| DEBUG [U=740536,P=13639] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| VERBOSE [U=740536,P=13639] sexec.c:62:main() : Checking that we are allowed to run as SUID | |
| DEBUG [U=740536,P=13639] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(allow setuid, 1) | |
| DEBUG [U=740536,P=13639] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(allow setuid) | |
| VERBOSE [U=740536,P=13639] config_parser.c:91:singularity_config_get_value(): Got config key allow setuid (= 'yes') | |
| DEBUG [U=740536,P=13639] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(allow setuid, 1) = 1 | |
| VERBOSE [U=740536,P=13639] sexec.c:67:main() : Checking if we were requested to run as NOSUID by user | |
| DEBUG [U=740536,P=13639] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_NOSUID | |
| VERBOSE [U=740536,P=13639] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_NOSUID | |
| DEBUG [U=740536,P=13639] util/util.c:102:envar_path() : Checking environment variable is valid path: 'SINGULARITY_IMAGE' | |
| VERBOSE [U=740536,P=13639] util/util.c:50:envar() : Checking input from environment: 'SINGULARITY_IMAGE' | |
| DEBUG [U=740536,P=13639] util/util.c:52:envar() : Checking environment variable is defined: SINGULARITY_IMAGE | |
| DEBUG [U=740536,P=13639] util/util.c:58:envar() : Checking environment variable length (<= 4096): SINGULARITY_IMAGE | |
| DEBUG [U=740536,P=13639] util/util.c:64:envar() : Checking environment variable has allowed characters: SINGULARITY_IMAGE | |
| VERBOSE [U=740536,P=13639] util/util.c:87:envar() : Obtained input from environment 'SINGULARITY_IMAGE' = '/N/u/hayashis/Karst/download/python_3.6-2016-11-01-156ca2b5b15f.img' | |
| VERBOSE [U=740536,P=13639] util/util.c:50:envar() : Checking input from environment: 'SINGULARITY_COMMAND' | |
| DEBUG [U=740536,P=13639] util/util.c:52:envar() : Checking environment variable is defined: SINGULARITY_COMMAND | |
| DEBUG [U=740536,P=13639] util/util.c:58:envar() : Checking environment variable length (<= 10): SINGULARITY_COMMAND | |
| DEBUG [U=740536,P=13639] util/util.c:64:envar() : Checking environment variable has allowed characters: SINGULARITY_COMMAND | |
| VERBOSE [U=740536,P=13639] util/util.c:87:envar() : Obtained input from environment 'SINGULARITY_COMMAND' = 'exec' | |
| DEBUG [U=740536,P=13639] action.c:55:singularity_action_init() : Checking on action to run | |
| DEBUG [U=740536,P=13639] action.c:67:singularity_action_init() : Setting action to: exec | |
| DEBUG [U=740536,P=13639] action.c:95:singularity_action_init() : Getting current working directory path string | |
| DEBUG [U=740536,P=13639] rootfs.c:71:singularity_rootfs_init() : Checking on container source type | |
| DEBUG [U=740536,P=13639] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13639] rootfs.c:80:singularity_rootfs_init() : Figuring out where to mount Singularity container | |
| DEBUG [U=740536,P=13639] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(container dir) | |
| VERBOSE [U=740536,P=13639] config_parser.c:91:singularity_config_get_value(): Got config key container dir (= '/var/singularity/mnt') | |
| DEBUG [U=740536,P=13639] rootfs.c:86:singularity_rootfs_init() : Set image mount path to: /var/singularity/mnt | |
| DEBUG [U=740536,P=13639] image.c:52:rootfs_image_init() : Inializing container rootfs image subsystem | |
| DEBUG [U=740536,P=13639] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_WRITABLE | |
| VERBOSE [U=740536,P=13639] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_WRITABLE | |
| VERBOSE [U=740536,P=13639] image-util.c:48:singularity_image_check() : Checking file is a Singularity image | |
| DEBUG [U=740536,P=13639] image-util.c:59:singularity_image_check() : Checking if first line matches key | |
| VERBOSE [U=740536,P=13639] image-util.c:62:singularity_image_check() : File is a valid Singularity image | |
| DEBUG [U=740536,P=13639] sessiondir.c:60:singularity_sessiondir_init(): Checking Singularity configuration for 'sessiondir prefix' | |
| DEBUG [U=740536,P=13639] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13639] util/util.c:102:envar_path() : Checking environment variable is valid path: 'SINGULARITY_SESSIONDIR' | |
| VERBOSE [U=740536,P=13639] util/util.c:50:envar() : Checking input from environment: 'SINGULARITY_SESSIONDIR' | |
| DEBUG [U=740536,P=13639] util/util.c:52:envar() : Checking environment variable is defined: SINGULARITY_SESSIONDIR | |
| VERBOSE [U=740536,P=13639] util/util.c:54:envar() : Environment variable is NULL: SINGULARITY_SESSIONDIR | |
| DEBUG [U=740536,P=13639] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(sessiondir prefix) | |
| DEBUG [U=740536,P=13639] config_parser.c:99:singularity_config_get_value(): No configuration file entry found for 'sessiondir prefix' | |
| DEBUG [U=740536,P=13639] sessiondir.c:75:singularity_sessiondir_init(): Set sessiondir to: /tmp/.singularity-session-740536.29.306323819 | |
| DEBUG [U=740536,P=13639] util/file.c:245:s_mkpath() : Creating directory: /tmp/.singularity-session-740536.29.306323819 | |
| DEBUG [U=740536,P=13639] sessiondir.c:91:singularity_sessiondir_init(): Opening sessiondir file descriptor | |
| DEBUG [U=740536,P=13639] sessiondir.c:97:singularity_sessiondir_init(): Setting shared flock() on session directory | |
| DEBUG [U=740536,P=13639] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_NOSESSIONCLEANUP | |
| VERBOSE [U=740536,P=13639] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_NOSESSIONCLEANUP | |
| DEBUG [U=740536,P=13639] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_NOCLEANUP | |
| VERBOSE [U=740536,P=13639] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_NOCLEANUP | |
| VERBOSE [U=740536,P=13639] fork.c:74:singularity_fork() : Forking child process | |
| VERBOSE [U=740536,P=13639] fork.c:90:singularity_fork() : Hello from parent process | |
| DEBUG [U=740536,P=13639] fork.c:109:singularity_fork() : Assigning sigaction()s | |
| DEBUG [U=740536,P=13639] fork.c:140:singularity_fork() : Creating generic signal pipes | |
| DEBUG [U=740536,P=13639] fork.c:148:singularity_fork() : Creating sigcld signal pipes | |
| DEBUG [U=740536,P=13639] fork.c:170:singularity_fork() : Waiting on signal from watchdog | |
| VERBOSE [U=740536,P=13642] fork.c:78:singularity_fork() : Hello from child process | |
| DEBUG [U=740536,P=13642] fork.c:81:singularity_fork() : Closing watchdog write pipe | |
| DEBUG [U=740536,P=13642] fork.c:86:singularity_fork() : Child process is returning control to process thread | |
| DEBUG [U=740536,P=13642] ns.c:45:singularity_ns_unshare() : Unsharing all namespaces | |
| VERBOSE [U=740536,P=13642] user.c:61:singularity_ns_user_unshare() : Not virtualizing user namespace: running SUID root | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(allow pid ns, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(allow pid ns) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key allow pid ns (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(allow pid ns, 1) = 1 | |
| DEBUG [U=740536,P=13642] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_UNSHARE_PID | |
| VERBOSE [U=740536,P=13642] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_UNSHARE_PID | |
| VERBOSE [U=740536,P=13642] pid.c:59:singularity_ns_pid_unshare() : Not virtualizing PID namespace on user request | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(mount slave, 0) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(mount slave) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key mount slave (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(mount slave, 0) = 1 | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| DEBUG [U=0,P=13642] mnt.c:54:singularity_ns_mnt_unshare() : Virtualizing FS namespace | |
| DEBUG [U=0,P=13642] mnt.c:61:singularity_ns_mnt_unshare() : Virtualizing mount namespace | |
| DEBUG [U=0,P=13642] mnt.c:70:singularity_ns_mnt_unshare() : Making mounts slave | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(allow ipc ns, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(allow ipc ns) | |
| DEBUG [U=740536,P=13642] config_parser.c:99:singularity_config_get_value(): No configuration file entry found for 'allow ipc ns' | |
| DEBUG [U=740536,P=13642] config_parser.c:126:singularity_config_get_bool(): Undefined configuration for 'allow ipc ns', returning default: yes | |
| DEBUG [U=740536,P=13642] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_UNSHARE_IPC | |
| VERBOSE [U=740536,P=13642] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_UNSHARE_IPC | |
| VERBOSE [U=740536,P=13642] ipc.c:59:singularity_ns_ipc_unshare() : Not virtualizing IPC namespace on user request | |
| DEBUG [U=740536,P=13642] rootfs.c:117:singularity_rootfs_mount() : Mounting image | |
| DEBUG [U=740536,P=13642] rootfs.c:119:singularity_rootfs_mount() : Checking for rootfs_source directory: /var/singularity/mnt/source | |
| DEBUG [U=740536,P=13642] rootfs.c:130:singularity_rootfs_mount() : Checking for overlay_mount directory: /var/singularity/mnt/overlay | |
| DEBUG [U=740536,P=13642] rootfs.c:141:singularity_rootfs_mount() : Checking for overlay_final directory: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] image.c:119:rootfs_image_mount() : Binding image to loop device | |
| DEBUG [U=740536,P=13642] sessiondir.c:149:singularity_sessiondir_get(): Returning: /tmp/.singularity-session-740536.29.306323819 | |
| DEBUG [U=740536,P=13642] loop-control.c:65:singularity_loop_bind() : Opening image loop device file: /tmp/.singularity-session-740536.29.306323819/image_loop_dev | |
| DEBUG [U=740536,P=13642] loop-control.c:71:singularity_loop_bind() : Requesting exclusive flock() on loop_dev lockfile | |
| DEBUG [U=740536,P=13642] loop-control.c:94:singularity_loop_bind() : Calculating image offset | |
| VERBOSE [U=740536,P=13642] image-util.c:77:singularity_image_offset() : Calculating image offset | |
| VERBOSE [U=740536,P=13642] image-util.c:86:singularity_image_offset() : Found image at an offset of 31 bytes | |
| DEBUG [U=740536,P=13642] image-util.c:91:singularity_image_offset() : Returning image_offset(image_fp) = 31 | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| DEBUG [U=0,P=13642] loop-control.c:101:singularity_loop_bind() : Finding next available loop device... | |
| VERBOSE [U=0,P=13642] loop-control.c:133:singularity_loop_bind() : Found avaialble loop device: /dev/loop0 | |
| DEBUG [U=0,P=13642] loop-control.c:135:singularity_loop_bind() : Setting loop device flags | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| VERBOSE [U=740536,P=13642] loop-control.c:145:singularity_loop_bind() : Using loop device: /dev/loop0 | |
| DEBUG [U=740536,P=13642] loop-control.c:147:singularity_loop_bind() : Writing active loop device name (/dev/loop0) to loop file cache: /tmp/.singularity-session-740536.29.306323819/image_loop_dev | |
| DEBUG [U=740536,P=13642] util/file.c:327:fileput() : Called fileput(/tmp/.singularity-session-740536.29.306323819/image_loop_dev, /dev/loop0) | |
| DEBUG [U=740536,P=13642] loop-control.c:153:singularity_loop_bind() : Resetting exclusive flock() to shared on image_loop_file | |
| DEBUG [U=740536,P=13642] loop-control.c:156:singularity_loop_bind() : Returning singularity_loop_bind(image_fp) = loop_fp | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] image.c:136:rootfs_image_mount() : Mounting image in read/only | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] rootfs.c:222:singularity_rootfs_mount() : Binding the ROOTFS_SOURCE to OVERLAY_FINAL (/var/singularity/mnt/source->/var/singularity/mnt/final) | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] rootfs.c:235:singularity_rootfs_check() : Checking if container has /bin/sh... | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] sessiondir.c:149:singularity_sessiondir_get(): Returning: /tmp/.singularity-session-740536.29.306323819 | |
| DEBUG [U=740536,P=13642] passwd.c:53:singularity_file_passwd() : Called singularity_file_passwd_create() | |
| DEBUG [U=740536,P=13642] passwd.c:70:singularity_file_passwd() : Checking configuration option: 'config passwd' | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(config passwd, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(config passwd) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key config passwd (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(config passwd, 1) = 1 | |
| VERBOSE [U=740536,P=13642] passwd.c:80:singularity_file_passwd() : Checking for template passwd file: /var/singularity/mnt/final/etc/passwd | |
| VERBOSE [U=740536,P=13642] passwd.c:86:singularity_file_passwd() : Creating template of /etc/passwd | |
| DEBUG [U=740536,P=13642] util/file.c:277:copy_file() : Called copy_file(/var/singularity/mnt/final/etc/passwd, /tmp/.singularity-session-740536.29.306323819/passwd) | |
| DEBUG [U=740536,P=13642] util/file.c:284:copy_file() : Opening source file: /var/singularity/mnt/final/etc/passwd | |
| DEBUG [U=740536,P=13642] util/file.c:290:copy_file() : Opening destination file: /tmp/.singularity-session-740536.29.306323819/passwd | |
| DEBUG [U=740536,P=13642] util/file.c:297:copy_file() : Calling fstat() on source file descriptor: 11 | |
| DEBUG [U=740536,P=13642] util/file.c:303:copy_file() : Cloning permission string of source to dest | |
| DEBUG [U=740536,P=13642] util/file.c:309:copy_file() : Copying file data... | |
| DEBUG [U=740536,P=13642] util/file.c:314:copy_file() : Done copying data, closing file pointers | |
| DEBUG [U=740536,P=13642] util/file.c:318:copy_file() : Returning copy_file(/var/singularity/mnt/final/etc/passwd, /tmp/.singularity-session-740536.29.306323819/passwd) = 0 | |
| DEBUG [U=740536,P=13642] passwd.c:92:singularity_file_passwd() : Opening the template passwd file: /tmp/.singularity-session-740536.29.306323819/passwd | |
| VERBOSE [U=740536,P=13642] passwd.c:98:singularity_file_passwd() : Creating template passwd file and appending user data | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] file-bind.c:41:container_file_bind() : Called file_bind(/tmp/.singularity-session-740536.29.306323819/passwd, /etc/passwd() | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] file-bind.c:61:container_file_bind() : Binding file '/tmp/.singularity-session-740536.29.306323819/passwd' to '/var/singularity/mnt/final/etc/passwd' | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] sessiondir.c:149:singularity_sessiondir_get(): Returning: /tmp/.singularity-session-740536.29.306323819 | |
| DEBUG [U=740536,P=13642] group.c:58:singularity_file_group() : Called singularity_file_group_create() | |
| DEBUG [U=740536,P=13642] group.c:75:singularity_file_group() : Checking configuration option: 'config group' | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(config group, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(config group) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key config group (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(config group, 1) = 1 | |
| VERBOSE [U=740536,P=13642] group.c:102:singularity_file_group() : Creating template of /etc/group for containment | |
| DEBUG [U=740536,P=13642] util/file.c:277:copy_file() : Called copy_file(/var/singularity/mnt/final/etc/group, /tmp/.singularity-session-740536.29.306323819/group) | |
| DEBUG [U=740536,P=13642] util/file.c:284:copy_file() : Opening source file: /var/singularity/mnt/final/etc/group | |
| DEBUG [U=740536,P=13642] util/file.c:290:copy_file() : Opening destination file: /tmp/.singularity-session-740536.29.306323819/group | |
| DEBUG [U=740536,P=13642] util/file.c:297:copy_file() : Calling fstat() on source file descriptor: 12 | |
| DEBUG [U=740536,P=13642] util/file.c:303:copy_file() : Cloning permission string of source to dest | |
| DEBUG [U=740536,P=13642] util/file.c:309:copy_file() : Copying file data... | |
| DEBUG [U=740536,P=13642] util/file.c:314:copy_file() : Done copying data, closing file pointers | |
| DEBUG [U=740536,P=13642] util/file.c:318:copy_file() : Returning copy_file(/var/singularity/mnt/final/etc/group, /tmp/.singularity-session-740536.29.306323819/group) = 0 | |
| VERBOSE [U=740536,P=13642] group.c:115:singularity_file_group() : Updating group file with user info | |
| DEBUG [U=740536,P=13642] group.c:127:singularity_file_group() : Getting supplementary group info | |
| DEBUG [U=740536,P=13642] group.c:131:singularity_file_group() : Skipping duplicate supplementary group | |
| VERBOSE [U=740536,P=13642] group.c:139:singularity_file_group() : Found supplementary group membership in: 1088 | |
| VERBOSE [U=740536,P=13642] group.c:140:singularity_file_group() : Adding user's supplementary group ('lifebid') info to template group file | |
| VERBOSE [U=740536,P=13642] group.c:139:singularity_file_group() : Found supplementary group membership in: 1160 | |
| VERBOSE [U=740536,P=13642] group.c:140:singularity_file_group() : Adding user's supplementary group ('brainlife') info to template group file | |
| VERBOSE [U=740536,P=13642] group.c:139:singularity_file_group() : Found supplementary group membership in: 1163 | |
| VERBOSE [U=740536,P=13642] group.c:140:singularity_file_group() : Adding user's supplementary group ('o3d') info to template group file | |
| VERBOSE [U=740536,P=13642] group.c:139:singularity_file_group() : Found supplementary group membership in: 2001 | |
| VERBOSE [U=740536,P=13642] group.c:140:singularity_file_group() : Adding user's supplementary group ('hpc') info to template group file | |
| VERBOSE [U=740536,P=13642] group.c:139:singularity_file_group() : Found supplementary group membership in: 2056 | |
| VERBOSE [U=740536,P=13642] group.c:140:singularity_file_group() : Adding user's supplementary group ('emcenter') info to template group file | |
| VERBOSE [U=740536,P=13642] group.c:139:singularity_file_group() : Found supplementary group membership in: 4146 | |
| VERBOSE [U=740536,P=13642] group.c:140:singularity_file_group() : Adding user's supplementary group ('gaus') info to template group file | |
| VERBOSE [U=740536,P=13642] group.c:139:singularity_file_group() : Found supplementary group membership in: 4160 | |
| VERBOSE [U=740536,P=13642] group.c:140:singularity_file_group() : Adding user's supplementary group ('odi') info to template group file | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] file-bind.c:41:container_file_bind() : Called file_bind(/tmp/.singularity-session-740536.29.306323819/group, /etc/group() | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] file-bind.c:61:container_file_bind() : Binding file '/tmp/.singularity-session-740536.29.306323819/group' to '/var/singularity/mnt/final/etc/group' | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] resolvconf.c:47:singularity_file_resolvconf(): Checking configuration option | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(config resolv_conf, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(config resolv_conf) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key config resolv_conf (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(config resolv_conf, 1) = 1 | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] file-bind.c:41:container_file_bind() : Called file_bind(/etc/resolv.conf, /etc/resolv.conf() | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] file-bind.c:61:container_file_bind() : Binding file '/etc/resolv.conf' to '/var/singularity/mnt/final/etc/resolv.conf' | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(mount hostfs, 0) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(mount hostfs) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key mount hostfs (= 'no') | |
| DEBUG [U=740536,P=13642] config_parser.c:118:singularity_config_get_bool(): Return singularity_config_get_bool(mount hostfs, 0) = 0 | |
| DEBUG [U=740536,P=13642] hostfs.c:53:singularity_mount_hostfs() : Not mounting host file systems per configuration | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_CONTAIN | |
| VERBOSE [U=740536,P=13642] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_CONTAIN | |
| DEBUG [U=740536,P=13642] binds.c:48:singularity_mount_binds() : Checking configuration file for 'bind path' | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(bind path) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key bind path (= '/etc/hosts') | |
| VERBOSE [U=740536,P=13642] binds.c:63:singularity_mount_binds() : Found 'bind path' = /etc/hosts, /etc/hosts | |
| DEBUG [U=740536,P=13642] binds.c:70:singularity_mount_binds() : Checking if bind point is already mounted: /etc/hosts | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] mount-util.c:42:check_mounted() : Opening /proc/mounts | |
| DEBUG [U=740536,P=13642] mount-util.c:48:check_mounted() : Iterating through /proc/mounts | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] binds.c:112:singularity_mount_binds() : Binding '/etc/hosts' to '/var/singularity/mnt/final//etc/hosts' | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(bind path) | |
| DEBUG [U=740536,P=13642] config_parser.c:99:singularity_config_get_value(): No configuration file entry found for 'bind path' | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] kernelfs.c:43:singularity_mount_kernelfs() : Checking configuration file for 'mount proc' | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(mount proc, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(mount proc) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key mount proc (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(mount proc, 1) = 1 | |
| DEBUG [U=740536,P=13642] pid.c:46:singularity_ns_pid_enabled() : Checking PID namespace enabled: -1 | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] kernelfs.c:57:singularity_mount_kernelfs() : Bind mounting /proc | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] kernelfs.c:73:singularity_mount_kernelfs() : Checking configuration file for 'mount sys' | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(mount sys, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(mount sys) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key mount sys (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(mount sys, 1) = 1 | |
| DEBUG [U=740536,P=13642] user.c:45:singularity_ns_user_enabled() : Checking user namespace enabled: -1 | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] kernelfs.c:79:singularity_mount_kernelfs() : Mounting /sys | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(mount dev) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key mount dev (= 'yes') | |
| DEBUG [U=740536,P=13642] dev.c:91:singularity_mount_dev() : Checking configuration file for 'mount dev' | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(mount dev, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(mount dev) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key mount dev (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(mount dev, 1) = 1 | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] dev.c:96:singularity_mount_dev() : Bind mounting /dev | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(mount tmp, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(mount tmp) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key mount tmp (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(mount tmp, 1) = 1 | |
| DEBUG [U=740536,P=13642] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_CONTAIN | |
| VERBOSE [U=740536,P=13642] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_CONTAIN | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] tmp.c:80:singularity_mount_tmp() : Mounting directory: /tmp | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] tmp.c:100:singularity_mount_tmp() : Mounting directory: /var/tmp | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] sessiondir.c:149:singularity_sessiondir_get(): Returning: /tmp/.singularity-session-740536.29.306323819 | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(mount home, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(mount home) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key mount home (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(mount home, 1) = 1 | |
| DEBUG [U=740536,P=13642] home.c:69:singularity_mount_home() : Obtaining user's homedir | |
| DEBUG [U=740536,P=13642] home.c:72:singularity_mount_home() : Checking if home directory is already mounted: /N/u/hayashis/Karst | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] mount-util.c:42:check_mounted() : Opening /proc/mounts | |
| DEBUG [U=740536,P=13642] mount-util.c:48:check_mounted() : Iterating through /proc/mounts | |
| DEBUG [U=740536,P=13642] util/util.c:102:envar_path() : Checking environment variable is valid path: 'SINGULARITY_HOME' | |
| VERBOSE [U=740536,P=13642] util/util.c:50:envar() : Checking input from environment: 'SINGULARITY_HOME' | |
| DEBUG [U=740536,P=13642] util/util.c:52:envar() : Checking environment variable is defined: SINGULARITY_HOME | |
| VERBOSE [U=740536,P=13642] util/util.c:54:envar() : Environment variable is NULL: SINGULARITY_HOME | |
| DEBUG [U=740536,P=13642] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_CONTAIN | |
| VERBOSE [U=740536,P=13642] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_CONTAIN | |
| VERBOSE [U=740536,P=13642] home.c:112:singularity_mount_home() : Set base the home directory source to: /N/u/hayashis/Karst | |
| DEBUG [U=740536,P=13642] util/file.c:245:s_mkpath() : Creating directory: /tmp/.singularity-session-740536.29.306323819/N | |
| DEBUG [U=740536,P=13642] util/file.c:245:s_mkpath() : Creating directory: /tmp/.singularity-session-740536.29.306323819/N/u | |
| DEBUG [U=740536,P=13642] util/file.c:245:s_mkpath() : Creating directory: /tmp/.singularity-session-740536.29.306323819/N/u/hayashis | |
| DEBUG [U=740536,P=13642] util/file.c:245:s_mkpath() : Creating directory: /tmp/.singularity-session-740536.29.306323819/N/u/hayashis/Karst | |
| DEBUG [U=740536,P=13642] home.c:129:singularity_mount_home() : Checking permissions on home directory: /N/u/hayashis/Karst | |
| DEBUG [U=740536,P=13642] home.c:136:singularity_mount_home() : Trying to create home dir within container | |
| DEBUG [U=740536,P=13642] rootfs.c:59:singularity_rootfs_overlay_enabled(): Returning singularity_rootfs_overlay: 0 | |
| DEBUG [U=740536,P=13642] util/file.c:386:basedir() : Obtaining basedir for: /N/u/hayashis/Karst | |
| DEBUG [U=740536,P=13642] util/file.c:389:basedir() : Iterating basedir: /N/u/hayashis/Karst | |
| DEBUG [U=740536,P=13642] util/file.c:389:basedir() : Iterating basedir: /N/u/hayashis | |
| DEBUG [U=740536,P=13642] util/file.c:389:basedir() : Iterating basedir: /N/u | |
| DEBUG [U=740536,P=13642] util/file.c:389:basedir() : Iterating basedir: /N | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] home.c:160:singularity_mount_home() : Mounting home directory to stage: /N/u/hayashis/Karst->/tmp/.singularity-session-740536.29.306323819/N/u/hayashis/Karst | |
| VERBOSE [U=0,P=13642] home.c:166:singularity_mount_home() : Mounting staged home directory into container: /tmp/.singularity-session-740536.29.306323819/N->/var/singularity/mnt/final/N | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] userbinds.c:45:singularity_mount_userbinds(): Checking for environment variable 'SINGULARITY_BINDPATH' | |
| DEBUG [U=740536,P=13642] util/util.c:102:envar_path() : Checking environment variable is valid path: 'SINGULARITY_BINDPATH' | |
| VERBOSE [U=740536,P=13642] util/util.c:50:envar() : Checking input from environment: 'SINGULARITY_BINDPATH' | |
| DEBUG [U=740536,P=13642] util/util.c:52:envar() : Checking environment variable is defined: SINGULARITY_BINDPATH | |
| VERBOSE [U=740536,P=13642] util/util.c:54:envar() : Environment variable is NULL: SINGULARITY_BINDPATH | |
| DEBUG [U=740536,P=13642] userbinds.c:148:singularity_mount_userbinds(): No user bind mounts specified. | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] scratch.c:53:singularity_mount_scratch() : Getting SINGULARITY_SCRATCHDIR from environment | |
| DEBUG [U=740536,P=13642] util/util.c:102:envar_path() : Checking environment variable is valid path: 'SINGULARITY_SCRATCHDIR' | |
| VERBOSE [U=740536,P=13642] util/util.c:50:envar() : Checking input from environment: 'SINGULARITY_SCRATCHDIR' | |
| DEBUG [U=740536,P=13642] util/util.c:52:envar() : Checking environment variable is defined: SINGULARITY_SCRATCHDIR | |
| VERBOSE [U=740536,P=13642] util/util.c:54:envar() : Environment variable is NULL: SINGULARITY_SCRATCHDIR | |
| DEBUG [U=740536,P=13642] scratch.c:55:singularity_mount_scratch() : Not mounting scratch directory: Not requested | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] cwd.c:47:singularity_mount_cwd() : Checking to see if we should mount current working directory | |
| DEBUG [U=740536,P=13642] cwd.c:49:singularity_mount_cwd() : Getting current working directory | |
| DEBUG [U=740536,P=13642] cwd.c:55:singularity_mount_cwd() : Checking configuration file for 'user bind control' | |
| DEBUG [U=740536,P=13642] config_parser.c:62:singularity_config_rewind(): Rewinding configuration file | |
| DEBUG [U=740536,P=13642] config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(user bind control, 1) | |
| DEBUG [U=740536,P=13642] config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(user bind control) | |
| VERBOSE [U=740536,P=13642] config_parser.c:91:singularity_config_get_value(): Got config key user bind control (= 'yes') | |
| DEBUG [U=740536,P=13642] config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(user bind control, 1) = 1 | |
| DEBUG [U=740536,P=13642] cwd.c:67:singularity_mount_cwd() : Checking for contain option | |
| DEBUG [U=740536,P=13642] util/util.c:92:envar_defined() : Checking if environment variable is defined: SINGULARITY_CONTAIN | |
| VERBOSE [U=740536,P=13642] util/util.c:94:envar_defined() : Environment variable is undefined: SINGULARITY_CONTAIN | |
| DEBUG [U=740536,P=13642] cwd.c:73:singularity_mount_cwd() : Checking if CWD is already mounted: /N/dc2/scratch/hayashis/tmp/python36 | |
| DEBUG [U=740536,P=13642] rootfs.c:64:singularity_rootfs_dir() : Returning singularity_rootfs_dir: /var/singularity/mnt/final | |
| DEBUG [U=740536,P=13642] mount-util.c:42:check_mounted() : Opening /proc/mounts | |
| DEBUG [U=740536,P=13642] mount-util.c:48:check_mounted() : Iterating through /proc/mounts | |
| DEBUG [U=740536,P=13642] cwd.c:79:singularity_mount_cwd() : Checking if overlay is enabled | |
| DEBUG [U=740536,P=13642] rootfs.c:59:singularity_rootfs_overlay_enabled(): Returning singularity_rootfs_overlay: 0 | |
| VERBOSE [U=740536,P=13642] cwd.c:81:singularity_mount_cwd() : Not mounting current directory: overlay is not enabled | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| VERBOSE [U=0,P=13642] rootfs.c:248:singularity_rootfs_chroot() : Entering container file system root: /var/singularity/mnt/final | |
| DEBUG [U=0,P=13642] privilege.c:179:singularity_priv_drop() : Dropping privileges to UID=740536, GID=236 | |
| DEBUG [U=740536,P=13642] privilege.c:191:singularity_priv_drop() : Confirming we have correct UID/GID | |
| DEBUG [U=740536,P=13642] rootfs.c:255:singularity_rootfs_chroot() : Changing dir to '/' within the new root | |
| DEBUG [U=740536,P=13642] privilege.c:216:singularity_priv_drop_perm(): Called singularity_priv_drop_perm(void) | |
| DEBUG [U=740536,P=13642] privilege.c:233:singularity_priv_drop_perm(): Escalating permissison so we can properly drop permission | |
| DEBUG [U=740536,P=13642] privilege.c:152:singularity_priv_escalate(): Temporarily escalating privileges (U=740536) | |
| DEBUG [U=0,P=13642] privilege.c:236:singularity_priv_drop_perm(): Resetting supplementary groups | |
| DEBUG [U=0,P=13642] privilege.c:242:singularity_priv_drop_perm(): Dropping to group ID '236' | |
| DEBUG [U=0,P=13642] privilege.c:248:singularity_priv_drop_perm(): Dropping real and effective privileges to GID = '236' | |
| DEBUG [U=0,P=13642] privilege.c:254:singularity_priv_drop_perm(): Dropping real and effective privileges to UID = '740536' | |
| DEBUG [U=740536,P=13642] privilege.c:260:singularity_priv_drop_perm(): Confirming we have correct GID | |
| DEBUG [U=740536,P=13642] privilege.c:266:singularity_priv_drop_perm(): Confirming we have correct UID | |
| DEBUG [U=740536,P=13642] privilege.c:274:singularity_priv_drop_perm(): Setting NO_NEW_PRIVS to prevent future privilege escalations. | |
| DEBUG [U=740536,P=13642] privilege.c:284:singularity_priv_drop_perm(): Finished dropping privileges | |
| DEBUG [U=740536,P=13642] action.c:108:singularity_action_do() : Trying to change directory to where we started | |
| DEBUG [U=740536,P=13642] util/util.c:102:envar_path() : Checking environment variable is valid path: 'SINGULARITY_TARGET_PWD' | |
| VERBOSE [U=740536,P=13642] util/util.c:50:envar() : Checking input from environment: 'SINGULARITY_TARGET_PWD' | |
| DEBUG [U=740536,P=13642] util/util.c:52:envar() : Checking environment variable is defined: SINGULARITY_TARGET_PWD | |
| VERBOSE [U=740536,P=13642] util/util.c:54:envar() : Environment variable is NULL: SINGULARITY_TARGET_PWD | |
| DEBUG [U=740536,P=13642] action.c:116:singularity_action_do() : Failed changing directory to: /N/dc2/scratch/hayashis/tmp/python36 | |
| VERBOSE [U=740536,P=13642] action.c:117:singularity_action_do() : Changing to home directory | |
| DEBUG [U=740536,P=13642] action.c:121:singularity_action_do() : Obtaining user's homedir | |
| DEBUG [U=740536,P=13642] action.c:139:singularity_action_do() : Running action: exec | |
| VERBOSE [U=740536,P=13642] exec.c:40:action_exec_do() : Exec'ing /.exec | |
| /.exec: 3: exec: test.py: not found | |
| DEBUG [U=740536,P=13639] fork.c:52:handle_sigchld() : Checking child pids: 13642 13642 | |
| DEBUG [U=740536,P=13639] fork.c:54:handle_sigchld() : Forwarding signal through sigchld_signal_wpipe | |
| DEBUG [U=740536,P=13639] fork.c:196:singularity_fork() : Parent process is exiting | |
| DEBUG [U=740536,P=13639] util/util.c:102:envar_path() : Checking environment variable is valid path: 'SINGULARITY_RUNDIR' | |
| VERBOSE [U=740536,P=13639] util/util.c:50:envar() : Checking input from environment: 'SINGULARITY_RUNDIR' | |
| DEBUG [U=740536,P=13639] util/util.c:52:envar() : Checking environment variable is defined: SINGULARITY_RUNDIR | |
| VERBOSE [U=740536,P=13639] util/util.c:54:envar() : Environment variable is NULL: SINGULARITY_RUNDIR | |
| DEBUG [U=740536,P=13639] sessiondir.c:111:singularity_sessiondir_init(): Cleanup thread waiting on child... | |
| DEBUG [U=740536,P=13639] sessiondir.c:116:singularity_sessiondir_init(): Checking to see if we are the last process running in this sessiondir | |
| VERBOSE [U=740536,P=13639] sessiondir.c:118:singularity_sessiondir_init(): Cleaning sessiondir: /tmp/.singularity-session-740536.29.306323819 | |
| DEBUG [U=740536,P=13639] util/file.c:267:s_rmdir() : Removing directory: /tmp/.singularity-session-740536.29.306323819 |
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