Process hangs before termination with ubuntu 18.04












3















When using ABAQUS 6.14 (but also ABAQUS 2018) on ubuntu 18.04 everything seems to work fine except the termination of the standard process (the process started when performing an implicit analysis -- if you are not familiar with this it doesn't matter).



The analysis indeed works as one can also see in a log file (the .sta file, for those who are familiar with abaqus) the message THE ANALYSIS HAS COMPLETED SUCCESSFULLY. The output database contains the analysis results. However, after the analysis has been completed, the process standard remains in a sleeping status using 0% CPU and keeping the same amount of RAM as when it was running.



From strace I get:



[pid 23191] close(8)                    = 0
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
[pid 23193] <... futex resumed> ) = 0
[pid 23191] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23191] munmap(0x7f3ab130b000, 327680) = 0
[pid 23191] munmap(0x7f3ab136b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab16db000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0fbb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0ddb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0a0b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab03fb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab050b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab00cb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab02eb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab14eb000, 1114112) = 0
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 8, NULL) = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 12, NULL <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>


Like if the two processes were in a deadlock state. Moreover, the commands



pid -p 7002


and



pid -p 7010


do give an empty output. The dirs /proc/7002 and /proc/7010 do not exist.



The only abaqus-related processes executing are



david  6995  0.0  0.1 295428 51388 pts/0    S    17:00   0:00 /opt/abaqus/6.14-1/code/bin/python /opt/abaqus/6.14-1
david 6998 0.0 0.2 368744 97948 pts/0 S 17:00 0:00 /opt/abaqus/6.14-1/code/bin/python std_inst.com
david 7001 0.1 0.0 122076 20096 pts/0 Sl 17:00 0:03 /opt/abaqus/6.14-1/code/bin/eliT_DriverLM -job std_in
david 7008 0.4 0.5 735812 185364 pts/0 Sl 17:00 0:07 /opt/abaqus/6.14-1/code/bin/standard -standard -acade


On ubuntu 16.04 the exact same version works like a charm. Here the same strace on ubuntu 16.04 (with the same kernel version as my 18.04, i.e. 4.15.0-29):



3890  close(8)                          = 0
3892 <... select resumed> ) = 0 (Timeout)
3892 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3892 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3892 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3892 <... futex resumed> ) = 0
3890 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 select(7, [4 5 6], NULL, NULL, {0, 20000} <unfinished ...>
3890 munmap(0x7f29c7adb000, 327680) = 0
3890 munmap(0x7f29c7b3b000, 1114112) = 0
3890 munmap(0x7f29c7eab000, 1114112) = 0
3890 munmap(0x7f29c778b000, 1114112) = 0
3890 munmap(0x7f29c75ab000, 1114112) = 0
3890 munmap(0x7f29c71db000, 1114112) = 0
3890 munmap(0x7f29c6bcb000, 1114112) = 0
3890 munmap(0x7f29c6cdb000, 1114112) = 0
3890 munmap(0x7f29c689b000, 1114112) = 0
3890 munmap(0x7f29c6abb000, 1114112) = 0
3890 munmap(0x7f29c7cbb000, 1114112) = 0
3890 exit_group(0) = ?
3891 +++ exited with 0 +++
3893 +++ exited with 0 +++
3892 +++ exited with 0 +++
3890 +++ exited with 0 +++
3880 <... wait4 resumed> [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 3890
3880 --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=3890, si_uid=1000, si_status=0, si_utime=107, si_stime=7} ---


Has someone a good idea how to solve this? Or in which direction should I investigate further.










share|improve this question


















  • 1





    I can confirm the problem. However, the problem does not exist on an Ubuntu 16.04 system with 4.15 mainline Kernel.

    – Christoph90
    Aug 7 '18 at 7:15











  • I too have this problem. I ran strace on the child processes and there is a deadlock somewhere.

    – user90855
    Oct 6 '18 at 16:50
















3















When using ABAQUS 6.14 (but also ABAQUS 2018) on ubuntu 18.04 everything seems to work fine except the termination of the standard process (the process started when performing an implicit analysis -- if you are not familiar with this it doesn't matter).



The analysis indeed works as one can also see in a log file (the .sta file, for those who are familiar with abaqus) the message THE ANALYSIS HAS COMPLETED SUCCESSFULLY. The output database contains the analysis results. However, after the analysis has been completed, the process standard remains in a sleeping status using 0% CPU and keeping the same amount of RAM as when it was running.



From strace I get:



[pid 23191] close(8)                    = 0
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
[pid 23193] <... futex resumed> ) = 0
[pid 23191] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23191] munmap(0x7f3ab130b000, 327680) = 0
[pid 23191] munmap(0x7f3ab136b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab16db000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0fbb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0ddb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0a0b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab03fb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab050b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab00cb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab02eb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab14eb000, 1114112) = 0
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 8, NULL) = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 12, NULL <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>


Like if the two processes were in a deadlock state. Moreover, the commands



pid -p 7002


and



pid -p 7010


do give an empty output. The dirs /proc/7002 and /proc/7010 do not exist.



The only abaqus-related processes executing are



david  6995  0.0  0.1 295428 51388 pts/0    S    17:00   0:00 /opt/abaqus/6.14-1/code/bin/python /opt/abaqus/6.14-1
david 6998 0.0 0.2 368744 97948 pts/0 S 17:00 0:00 /opt/abaqus/6.14-1/code/bin/python std_inst.com
david 7001 0.1 0.0 122076 20096 pts/0 Sl 17:00 0:03 /opt/abaqus/6.14-1/code/bin/eliT_DriverLM -job std_in
david 7008 0.4 0.5 735812 185364 pts/0 Sl 17:00 0:07 /opt/abaqus/6.14-1/code/bin/standard -standard -acade


On ubuntu 16.04 the exact same version works like a charm. Here the same strace on ubuntu 16.04 (with the same kernel version as my 18.04, i.e. 4.15.0-29):



3890  close(8)                          = 0
3892 <... select resumed> ) = 0 (Timeout)
3892 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3892 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3892 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3892 <... futex resumed> ) = 0
3890 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 select(7, [4 5 6], NULL, NULL, {0, 20000} <unfinished ...>
3890 munmap(0x7f29c7adb000, 327680) = 0
3890 munmap(0x7f29c7b3b000, 1114112) = 0
3890 munmap(0x7f29c7eab000, 1114112) = 0
3890 munmap(0x7f29c778b000, 1114112) = 0
3890 munmap(0x7f29c75ab000, 1114112) = 0
3890 munmap(0x7f29c71db000, 1114112) = 0
3890 munmap(0x7f29c6bcb000, 1114112) = 0
3890 munmap(0x7f29c6cdb000, 1114112) = 0
3890 munmap(0x7f29c689b000, 1114112) = 0
3890 munmap(0x7f29c6abb000, 1114112) = 0
3890 munmap(0x7f29c7cbb000, 1114112) = 0
3890 exit_group(0) = ?
3891 +++ exited with 0 +++
3893 +++ exited with 0 +++
3892 +++ exited with 0 +++
3890 +++ exited with 0 +++
3880 <... wait4 resumed> [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 3890
3880 --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=3890, si_uid=1000, si_status=0, si_utime=107, si_stime=7} ---


Has someone a good idea how to solve this? Or in which direction should I investigate further.










share|improve this question


















  • 1





    I can confirm the problem. However, the problem does not exist on an Ubuntu 16.04 system with 4.15 mainline Kernel.

    – Christoph90
    Aug 7 '18 at 7:15











  • I too have this problem. I ran strace on the child processes and there is a deadlock somewhere.

    – user90855
    Oct 6 '18 at 16:50














3












3








3


1






When using ABAQUS 6.14 (but also ABAQUS 2018) on ubuntu 18.04 everything seems to work fine except the termination of the standard process (the process started when performing an implicit analysis -- if you are not familiar with this it doesn't matter).



The analysis indeed works as one can also see in a log file (the .sta file, for those who are familiar with abaqus) the message THE ANALYSIS HAS COMPLETED SUCCESSFULLY. The output database contains the analysis results. However, after the analysis has been completed, the process standard remains in a sleeping status using 0% CPU and keeping the same amount of RAM as when it was running.



From strace I get:



[pid 23191] close(8)                    = 0
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
[pid 23193] <... futex resumed> ) = 0
[pid 23191] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23191] munmap(0x7f3ab130b000, 327680) = 0
[pid 23191] munmap(0x7f3ab136b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab16db000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0fbb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0ddb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0a0b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab03fb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab050b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab00cb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab02eb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab14eb000, 1114112) = 0
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 8, NULL) = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 12, NULL <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>


Like if the two processes were in a deadlock state. Moreover, the commands



pid -p 7002


and



pid -p 7010


do give an empty output. The dirs /proc/7002 and /proc/7010 do not exist.



The only abaqus-related processes executing are



david  6995  0.0  0.1 295428 51388 pts/0    S    17:00   0:00 /opt/abaqus/6.14-1/code/bin/python /opt/abaqus/6.14-1
david 6998 0.0 0.2 368744 97948 pts/0 S 17:00 0:00 /opt/abaqus/6.14-1/code/bin/python std_inst.com
david 7001 0.1 0.0 122076 20096 pts/0 Sl 17:00 0:03 /opt/abaqus/6.14-1/code/bin/eliT_DriverLM -job std_in
david 7008 0.4 0.5 735812 185364 pts/0 Sl 17:00 0:07 /opt/abaqus/6.14-1/code/bin/standard -standard -acade


On ubuntu 16.04 the exact same version works like a charm. Here the same strace on ubuntu 16.04 (with the same kernel version as my 18.04, i.e. 4.15.0-29):



3890  close(8)                          = 0
3892 <... select resumed> ) = 0 (Timeout)
3892 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3892 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3892 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3892 <... futex resumed> ) = 0
3890 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 select(7, [4 5 6], NULL, NULL, {0, 20000} <unfinished ...>
3890 munmap(0x7f29c7adb000, 327680) = 0
3890 munmap(0x7f29c7b3b000, 1114112) = 0
3890 munmap(0x7f29c7eab000, 1114112) = 0
3890 munmap(0x7f29c778b000, 1114112) = 0
3890 munmap(0x7f29c75ab000, 1114112) = 0
3890 munmap(0x7f29c71db000, 1114112) = 0
3890 munmap(0x7f29c6bcb000, 1114112) = 0
3890 munmap(0x7f29c6cdb000, 1114112) = 0
3890 munmap(0x7f29c689b000, 1114112) = 0
3890 munmap(0x7f29c6abb000, 1114112) = 0
3890 munmap(0x7f29c7cbb000, 1114112) = 0
3890 exit_group(0) = ?
3891 +++ exited with 0 +++
3893 +++ exited with 0 +++
3892 +++ exited with 0 +++
3890 +++ exited with 0 +++
3880 <... wait4 resumed> [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 3890
3880 --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=3890, si_uid=1000, si_status=0, si_utime=107, si_stime=7} ---


Has someone a good idea how to solve this? Or in which direction should I investigate further.










share|improve this question














When using ABAQUS 6.14 (but also ABAQUS 2018) on ubuntu 18.04 everything seems to work fine except the termination of the standard process (the process started when performing an implicit analysis -- if you are not familiar with this it doesn't matter).



The analysis indeed works as one can also see in a log file (the .sta file, for those who are familiar with abaqus) the message THE ANALYSIS HAS COMPLETED SUCCESSFULLY. The output database contains the analysis results. However, after the analysis has been completed, the process standard remains in a sleeping status using 0% CPU and keeping the same amount of RAM as when it was running.



From strace I get:



[pid 23191] close(8)                    = 0
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
[pid 23193] <... futex resumed> ) = 0
[pid 23191] <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23191] munmap(0x7f3ab130b000, 327680) = 0
[pid 23191] munmap(0x7f3ab136b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab16db000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0fbb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0ddb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0a0b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab03fb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab050b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab00cb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab02eb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab14eb000, 1114112) = 0
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 8, NULL) = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 12, NULL <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> ) = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> ) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>


Like if the two processes were in a deadlock state. Moreover, the commands



pid -p 7002


and



pid -p 7010


do give an empty output. The dirs /proc/7002 and /proc/7010 do not exist.



The only abaqus-related processes executing are



david  6995  0.0  0.1 295428 51388 pts/0    S    17:00   0:00 /opt/abaqus/6.14-1/code/bin/python /opt/abaqus/6.14-1
david 6998 0.0 0.2 368744 97948 pts/0 S 17:00 0:00 /opt/abaqus/6.14-1/code/bin/python std_inst.com
david 7001 0.1 0.0 122076 20096 pts/0 Sl 17:00 0:03 /opt/abaqus/6.14-1/code/bin/eliT_DriverLM -job std_in
david 7008 0.4 0.5 735812 185364 pts/0 Sl 17:00 0:07 /opt/abaqus/6.14-1/code/bin/standard -standard -acade


On ubuntu 16.04 the exact same version works like a charm. Here the same strace on ubuntu 16.04 (with the same kernel version as my 18.04, i.e. 4.15.0-29):



3890  close(8)                          = 0
3892 <... select resumed> ) = 0 (Timeout)
3892 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3892 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3892 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
3890 futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3892 <... futex resumed> ) = 0
3890 <... futex resumed> ) = -1 EAGAIN (Resource temporarily unavailable)
3890 futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892 select(7, [4 5 6], NULL, NULL, {0, 20000} <unfinished ...>
3890 munmap(0x7f29c7adb000, 327680) = 0
3890 munmap(0x7f29c7b3b000, 1114112) = 0
3890 munmap(0x7f29c7eab000, 1114112) = 0
3890 munmap(0x7f29c778b000, 1114112) = 0
3890 munmap(0x7f29c75ab000, 1114112) = 0
3890 munmap(0x7f29c71db000, 1114112) = 0
3890 munmap(0x7f29c6bcb000, 1114112) = 0
3890 munmap(0x7f29c6cdb000, 1114112) = 0
3890 munmap(0x7f29c689b000, 1114112) = 0
3890 munmap(0x7f29c6abb000, 1114112) = 0
3890 munmap(0x7f29c7cbb000, 1114112) = 0
3890 exit_group(0) = ?
3891 +++ exited with 0 +++
3893 +++ exited with 0 +++
3892 +++ exited with 0 +++
3890 +++ exited with 0 +++
3880 <... wait4 resumed> [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 3890
3880 --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=3890, si_uid=1000, si_status=0, si_utime=107, si_stime=7} ---


Has someone a good idea how to solve this? Or in which direction should I investigate further.







18.04 process strace






share|improve this question













share|improve this question











share|improve this question




share|improve this question










asked Aug 3 '18 at 15:43









DavidDavid

841213




841213








  • 1





    I can confirm the problem. However, the problem does not exist on an Ubuntu 16.04 system with 4.15 mainline Kernel.

    – Christoph90
    Aug 7 '18 at 7:15











  • I too have this problem. I ran strace on the child processes and there is a deadlock somewhere.

    – user90855
    Oct 6 '18 at 16:50














  • 1





    I can confirm the problem. However, the problem does not exist on an Ubuntu 16.04 system with 4.15 mainline Kernel.

    – Christoph90
    Aug 7 '18 at 7:15











  • I too have this problem. I ran strace on the child processes and there is a deadlock somewhere.

    – user90855
    Oct 6 '18 at 16:50








1




1





I can confirm the problem. However, the problem does not exist on an Ubuntu 16.04 system with 4.15 mainline Kernel.

– Christoph90
Aug 7 '18 at 7:15





I can confirm the problem. However, the problem does not exist on an Ubuntu 16.04 system with 4.15 mainline Kernel.

– Christoph90
Aug 7 '18 at 7:15













I too have this problem. I ran strace on the child processes and there is a deadlock somewhere.

– user90855
Oct 6 '18 at 16:50





I too have this problem. I ran strace on the child processes and there is a deadlock somewhere.

– user90855
Oct 6 '18 at 16:50










3 Answers
3






active

oldest

votes


















0














I met this problem with Linux mint 19 too.
Abaqus 6.14-5 installed in Linux Mint 19.
It cannot be terminated automatically but seen form .sta file, the analysis is completed.
I think this problem is related to the kernel.
By the way, do you find any solutions now?






share|improve this answer


























  • I know. The analysis is complete, but the process is not terminated properly. No, I haven't found a solution yet. Not sure if it's related to the kernel, since with the same kernel under ubuntu 16.04 it just works fine

    – David
    Nov 8 '18 at 20:40











  • Thanks, Maybe we can apply a bug report in the Linux community(not sure the name of it).

    – leileilei
    Nov 9 '18 at 9:16











  • Actually, I guess it's not related to a bug. Ubuntu is simply not a supported OS by Abaqus.

    – David
    Nov 12 '18 at 15:05











  • This should be a comment, not an answer @leileilei

    – Christoph90
    Dec 19 '18 at 11:36





















0














I found a solution that circumvents the deadlock by using a singularity container as proposed by Will Furnass here: http://learningpatterns.me/posts-output/2018-01-30-abaqus-singularity/



Although a bit complicated in the first place, it works like a charm when setup properly. I modified my aliases for abaqus on my host system (Manjaro/Arch linux) such that they point to the install in the singularity container and execute the command in the containers environment. However, since I need Intel Fortran Compiler, I generated a basic centos 7 container and modified it afterwards to install compilers and abaqus (v2019 in this case) rather than using the .def script as proposed by Will Furnass.



It takes some time to setup but now I have a container image I can work with on any system that runs singularity, which is quite nice :)



EDIT: I also tested copying a working install to a more recent linux system (and avoiding a fresh install of abaqus), I can confirm that this didn't work in my case (CentOS 7 install copied to Manajaro system).






share|improve this answer





















  • 3





    Welcome to Ask Ubuntu! While this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference.

    – terdon
    Jan 20 at 13:09



















0














I would like to present my work around for this issue. I've made a python wrapper for the abq2018 solver which checks the .sta file for completeness. Once the .sta file is complete, any process named standard will be killed. I've found that the solver exits gracefully when standard is killed and the analysis is complete.



This work around is not a perfect solution. Current issues with this work around:




  1. can't replace the abq2018 solver call directly

  2. will not work from GUI, must be run from the shell

  3. only parses job= argument

  4. you can only run one analysis at at time since all standard processes are killed

  5. abq will hang forever if .sta file is not created or modified


How to use this workaround:




  1. Create Python file named abq. Code for abq is detailed below. If you are using a solver other than abq2018, replace the line cmd = 'abq20xx.. with the solver that you are using.

  2. Make abq executable and available in your path. I placed abq in the Abaqus commands folder, then ran chmod +x abq

  3. Run an Abaqus standard job by executing abq job=Job-1. This will execute Job-1.inp, then this will kill the standard solver once Job-1.sta is completed.


Code for abq is below



#!/usr/bin/python
import subprocess
import sys
import time
arguments = sys.argv
jobname = arguments[1].split('job=')[-1]
cmd = 'abq2018 cpus=4 ask_delete=OFF background job=' + jobname
p = subprocess.call(cmd, shell=True)

complete = False
termination_criteria = [' THE ANALYSIS HAS COMPLETED SUCCESSFULLYn',
' THE ANALYSIS HAS NOT BEEN COMPLETEDn']

while complete is False:
# wait every 5 seconds
time.sleep(5)
try:
with open(jobname + '.sta', 'r') as f:
last = f.readlines()[-1]
if last in termination_criteria:
# this will kill any process named standard
subprocess.call('pgrep standard | xargs kill', shell=True)
complete = True
except IOError:
# model.sta has been deleted or doesn't exist
# try again in 5 seconds
time.sleep(5)






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    3 Answers
    3






    active

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    3 Answers
    3






    active

    oldest

    votes









    active

    oldest

    votes






    active

    oldest

    votes









    0














    I met this problem with Linux mint 19 too.
    Abaqus 6.14-5 installed in Linux Mint 19.
    It cannot be terminated automatically but seen form .sta file, the analysis is completed.
    I think this problem is related to the kernel.
    By the way, do you find any solutions now?






    share|improve this answer


























    • I know. The analysis is complete, but the process is not terminated properly. No, I haven't found a solution yet. Not sure if it's related to the kernel, since with the same kernel under ubuntu 16.04 it just works fine

      – David
      Nov 8 '18 at 20:40











    • Thanks, Maybe we can apply a bug report in the Linux community(not sure the name of it).

      – leileilei
      Nov 9 '18 at 9:16











    • Actually, I guess it's not related to a bug. Ubuntu is simply not a supported OS by Abaqus.

      – David
      Nov 12 '18 at 15:05











    • This should be a comment, not an answer @leileilei

      – Christoph90
      Dec 19 '18 at 11:36


















    0














    I met this problem with Linux mint 19 too.
    Abaqus 6.14-5 installed in Linux Mint 19.
    It cannot be terminated automatically but seen form .sta file, the analysis is completed.
    I think this problem is related to the kernel.
    By the way, do you find any solutions now?






    share|improve this answer


























    • I know. The analysis is complete, but the process is not terminated properly. No, I haven't found a solution yet. Not sure if it's related to the kernel, since with the same kernel under ubuntu 16.04 it just works fine

      – David
      Nov 8 '18 at 20:40











    • Thanks, Maybe we can apply a bug report in the Linux community(not sure the name of it).

      – leileilei
      Nov 9 '18 at 9:16











    • Actually, I guess it's not related to a bug. Ubuntu is simply not a supported OS by Abaqus.

      – David
      Nov 12 '18 at 15:05











    • This should be a comment, not an answer @leileilei

      – Christoph90
      Dec 19 '18 at 11:36
















    0












    0








    0







    I met this problem with Linux mint 19 too.
    Abaqus 6.14-5 installed in Linux Mint 19.
    It cannot be terminated automatically but seen form .sta file, the analysis is completed.
    I think this problem is related to the kernel.
    By the way, do you find any solutions now?






    share|improve this answer















    I met this problem with Linux mint 19 too.
    Abaqus 6.14-5 installed in Linux Mint 19.
    It cannot be terminated automatically but seen form .sta file, the analysis is completed.
    I think this problem is related to the kernel.
    By the way, do you find any solutions now?







    share|improve this answer














    share|improve this answer



    share|improve this answer








    edited Nov 7 '18 at 18:45

























    answered Nov 7 '18 at 18:38









    leileileileileilei

    6114




    6114













    • I know. The analysis is complete, but the process is not terminated properly. No, I haven't found a solution yet. Not sure if it's related to the kernel, since with the same kernel under ubuntu 16.04 it just works fine

      – David
      Nov 8 '18 at 20:40











    • Thanks, Maybe we can apply a bug report in the Linux community(not sure the name of it).

      – leileilei
      Nov 9 '18 at 9:16











    • Actually, I guess it's not related to a bug. Ubuntu is simply not a supported OS by Abaqus.

      – David
      Nov 12 '18 at 15:05











    • This should be a comment, not an answer @leileilei

      – Christoph90
      Dec 19 '18 at 11:36





















    • I know. The analysis is complete, but the process is not terminated properly. No, I haven't found a solution yet. Not sure if it's related to the kernel, since with the same kernel under ubuntu 16.04 it just works fine

      – David
      Nov 8 '18 at 20:40











    • Thanks, Maybe we can apply a bug report in the Linux community(not sure the name of it).

      – leileilei
      Nov 9 '18 at 9:16











    • Actually, I guess it's not related to a bug. Ubuntu is simply not a supported OS by Abaqus.

      – David
      Nov 12 '18 at 15:05











    • This should be a comment, not an answer @leileilei

      – Christoph90
      Dec 19 '18 at 11:36



















    I know. The analysis is complete, but the process is not terminated properly. No, I haven't found a solution yet. Not sure if it's related to the kernel, since with the same kernel under ubuntu 16.04 it just works fine

    – David
    Nov 8 '18 at 20:40





    I know. The analysis is complete, but the process is not terminated properly. No, I haven't found a solution yet. Not sure if it's related to the kernel, since with the same kernel under ubuntu 16.04 it just works fine

    – David
    Nov 8 '18 at 20:40













    Thanks, Maybe we can apply a bug report in the Linux community(not sure the name of it).

    – leileilei
    Nov 9 '18 at 9:16





    Thanks, Maybe we can apply a bug report in the Linux community(not sure the name of it).

    – leileilei
    Nov 9 '18 at 9:16













    Actually, I guess it's not related to a bug. Ubuntu is simply not a supported OS by Abaqus.

    – David
    Nov 12 '18 at 15:05





    Actually, I guess it's not related to a bug. Ubuntu is simply not a supported OS by Abaqus.

    – David
    Nov 12 '18 at 15:05













    This should be a comment, not an answer @leileilei

    – Christoph90
    Dec 19 '18 at 11:36







    This should be a comment, not an answer @leileilei

    – Christoph90
    Dec 19 '18 at 11:36















    0














    I found a solution that circumvents the deadlock by using a singularity container as proposed by Will Furnass here: http://learningpatterns.me/posts-output/2018-01-30-abaqus-singularity/



    Although a bit complicated in the first place, it works like a charm when setup properly. I modified my aliases for abaqus on my host system (Manjaro/Arch linux) such that they point to the install in the singularity container and execute the command in the containers environment. However, since I need Intel Fortran Compiler, I generated a basic centos 7 container and modified it afterwards to install compilers and abaqus (v2019 in this case) rather than using the .def script as proposed by Will Furnass.



    It takes some time to setup but now I have a container image I can work with on any system that runs singularity, which is quite nice :)



    EDIT: I also tested copying a working install to a more recent linux system (and avoiding a fresh install of abaqus), I can confirm that this didn't work in my case (CentOS 7 install copied to Manajaro system).






    share|improve this answer





















    • 3





      Welcome to Ask Ubuntu! While this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference.

      – terdon
      Jan 20 at 13:09
















    0














    I found a solution that circumvents the deadlock by using a singularity container as proposed by Will Furnass here: http://learningpatterns.me/posts-output/2018-01-30-abaqus-singularity/



    Although a bit complicated in the first place, it works like a charm when setup properly. I modified my aliases for abaqus on my host system (Manjaro/Arch linux) such that they point to the install in the singularity container and execute the command in the containers environment. However, since I need Intel Fortran Compiler, I generated a basic centos 7 container and modified it afterwards to install compilers and abaqus (v2019 in this case) rather than using the .def script as proposed by Will Furnass.



    It takes some time to setup but now I have a container image I can work with on any system that runs singularity, which is quite nice :)



    EDIT: I also tested copying a working install to a more recent linux system (and avoiding a fresh install of abaqus), I can confirm that this didn't work in my case (CentOS 7 install copied to Manajaro system).






    share|improve this answer





















    • 3





      Welcome to Ask Ubuntu! While this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference.

      – terdon
      Jan 20 at 13:09














    0












    0








    0







    I found a solution that circumvents the deadlock by using a singularity container as proposed by Will Furnass here: http://learningpatterns.me/posts-output/2018-01-30-abaqus-singularity/



    Although a bit complicated in the first place, it works like a charm when setup properly. I modified my aliases for abaqus on my host system (Manjaro/Arch linux) such that they point to the install in the singularity container and execute the command in the containers environment. However, since I need Intel Fortran Compiler, I generated a basic centos 7 container and modified it afterwards to install compilers and abaqus (v2019 in this case) rather than using the .def script as proposed by Will Furnass.



    It takes some time to setup but now I have a container image I can work with on any system that runs singularity, which is quite nice :)



    EDIT: I also tested copying a working install to a more recent linux system (and avoiding a fresh install of abaqus), I can confirm that this didn't work in my case (CentOS 7 install copied to Manajaro system).






    share|improve this answer















    I found a solution that circumvents the deadlock by using a singularity container as proposed by Will Furnass here: http://learningpatterns.me/posts-output/2018-01-30-abaqus-singularity/



    Although a bit complicated in the first place, it works like a charm when setup properly. I modified my aliases for abaqus on my host system (Manjaro/Arch linux) such that they point to the install in the singularity container and execute the command in the containers environment. However, since I need Intel Fortran Compiler, I generated a basic centos 7 container and modified it afterwards to install compilers and abaqus (v2019 in this case) rather than using the .def script as proposed by Will Furnass.



    It takes some time to setup but now I have a container image I can work with on any system that runs singularity, which is quite nice :)



    EDIT: I also tested copying a working install to a more recent linux system (and avoiding a fresh install of abaqus), I can confirm that this didn't work in my case (CentOS 7 install copied to Manajaro system).







    share|improve this answer














    share|improve this answer



    share|improve this answer








    edited Jan 19 at 13:03

























    answered Jan 19 at 12:57









    A. BernathA. Bernath

    11




    11








    • 3





      Welcome to Ask Ubuntu! While this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference.

      – terdon
      Jan 20 at 13:09














    • 3





      Welcome to Ask Ubuntu! While this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference.

      – terdon
      Jan 20 at 13:09








    3




    3





    Welcome to Ask Ubuntu! While this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference.

    – terdon
    Jan 20 at 13:09





    Welcome to Ask Ubuntu! While this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference.

    – terdon
    Jan 20 at 13:09











    0














    I would like to present my work around for this issue. I've made a python wrapper for the abq2018 solver which checks the .sta file for completeness. Once the .sta file is complete, any process named standard will be killed. I've found that the solver exits gracefully when standard is killed and the analysis is complete.



    This work around is not a perfect solution. Current issues with this work around:




    1. can't replace the abq2018 solver call directly

    2. will not work from GUI, must be run from the shell

    3. only parses job= argument

    4. you can only run one analysis at at time since all standard processes are killed

    5. abq will hang forever if .sta file is not created or modified


    How to use this workaround:




    1. Create Python file named abq. Code for abq is detailed below. If you are using a solver other than abq2018, replace the line cmd = 'abq20xx.. with the solver that you are using.

    2. Make abq executable and available in your path. I placed abq in the Abaqus commands folder, then ran chmod +x abq

    3. Run an Abaqus standard job by executing abq job=Job-1. This will execute Job-1.inp, then this will kill the standard solver once Job-1.sta is completed.


    Code for abq is below



    #!/usr/bin/python
    import subprocess
    import sys
    import time
    arguments = sys.argv
    jobname = arguments[1].split('job=')[-1]
    cmd = 'abq2018 cpus=4 ask_delete=OFF background job=' + jobname
    p = subprocess.call(cmd, shell=True)

    complete = False
    termination_criteria = [' THE ANALYSIS HAS COMPLETED SUCCESSFULLYn',
    ' THE ANALYSIS HAS NOT BEEN COMPLETEDn']

    while complete is False:
    # wait every 5 seconds
    time.sleep(5)
    try:
    with open(jobname + '.sta', 'r') as f:
    last = f.readlines()[-1]
    if last in termination_criteria:
    # this will kill any process named standard
    subprocess.call('pgrep standard | xargs kill', shell=True)
    complete = True
    except IOError:
    # model.sta has been deleted or doesn't exist
    # try again in 5 seconds
    time.sleep(5)






    share|improve this answer




























      0














      I would like to present my work around for this issue. I've made a python wrapper for the abq2018 solver which checks the .sta file for completeness. Once the .sta file is complete, any process named standard will be killed. I've found that the solver exits gracefully when standard is killed and the analysis is complete.



      This work around is not a perfect solution. Current issues with this work around:




      1. can't replace the abq2018 solver call directly

      2. will not work from GUI, must be run from the shell

      3. only parses job= argument

      4. you can only run one analysis at at time since all standard processes are killed

      5. abq will hang forever if .sta file is not created or modified


      How to use this workaround:




      1. Create Python file named abq. Code for abq is detailed below. If you are using a solver other than abq2018, replace the line cmd = 'abq20xx.. with the solver that you are using.

      2. Make abq executable and available in your path. I placed abq in the Abaqus commands folder, then ran chmod +x abq

      3. Run an Abaqus standard job by executing abq job=Job-1. This will execute Job-1.inp, then this will kill the standard solver once Job-1.sta is completed.


      Code for abq is below



      #!/usr/bin/python
      import subprocess
      import sys
      import time
      arguments = sys.argv
      jobname = arguments[1].split('job=')[-1]
      cmd = 'abq2018 cpus=4 ask_delete=OFF background job=' + jobname
      p = subprocess.call(cmd, shell=True)

      complete = False
      termination_criteria = [' THE ANALYSIS HAS COMPLETED SUCCESSFULLYn',
      ' THE ANALYSIS HAS NOT BEEN COMPLETEDn']

      while complete is False:
      # wait every 5 seconds
      time.sleep(5)
      try:
      with open(jobname + '.sta', 'r') as f:
      last = f.readlines()[-1]
      if last in termination_criteria:
      # this will kill any process named standard
      subprocess.call('pgrep standard | xargs kill', shell=True)
      complete = True
      except IOError:
      # model.sta has been deleted or doesn't exist
      # try again in 5 seconds
      time.sleep(5)






      share|improve this answer


























        0












        0








        0







        I would like to present my work around for this issue. I've made a python wrapper for the abq2018 solver which checks the .sta file for completeness. Once the .sta file is complete, any process named standard will be killed. I've found that the solver exits gracefully when standard is killed and the analysis is complete.



        This work around is not a perfect solution. Current issues with this work around:




        1. can't replace the abq2018 solver call directly

        2. will not work from GUI, must be run from the shell

        3. only parses job= argument

        4. you can only run one analysis at at time since all standard processes are killed

        5. abq will hang forever if .sta file is not created or modified


        How to use this workaround:




        1. Create Python file named abq. Code for abq is detailed below. If you are using a solver other than abq2018, replace the line cmd = 'abq20xx.. with the solver that you are using.

        2. Make abq executable and available in your path. I placed abq in the Abaqus commands folder, then ran chmod +x abq

        3. Run an Abaqus standard job by executing abq job=Job-1. This will execute Job-1.inp, then this will kill the standard solver once Job-1.sta is completed.


        Code for abq is below



        #!/usr/bin/python
        import subprocess
        import sys
        import time
        arguments = sys.argv
        jobname = arguments[1].split('job=')[-1]
        cmd = 'abq2018 cpus=4 ask_delete=OFF background job=' + jobname
        p = subprocess.call(cmd, shell=True)

        complete = False
        termination_criteria = [' THE ANALYSIS HAS COMPLETED SUCCESSFULLYn',
        ' THE ANALYSIS HAS NOT BEEN COMPLETEDn']

        while complete is False:
        # wait every 5 seconds
        time.sleep(5)
        try:
        with open(jobname + '.sta', 'r') as f:
        last = f.readlines()[-1]
        if last in termination_criteria:
        # this will kill any process named standard
        subprocess.call('pgrep standard | xargs kill', shell=True)
        complete = True
        except IOError:
        # model.sta has been deleted or doesn't exist
        # try again in 5 seconds
        time.sleep(5)






        share|improve this answer













        I would like to present my work around for this issue. I've made a python wrapper for the abq2018 solver which checks the .sta file for completeness. Once the .sta file is complete, any process named standard will be killed. I've found that the solver exits gracefully when standard is killed and the analysis is complete.



        This work around is not a perfect solution. Current issues with this work around:




        1. can't replace the abq2018 solver call directly

        2. will not work from GUI, must be run from the shell

        3. only parses job= argument

        4. you can only run one analysis at at time since all standard processes are killed

        5. abq will hang forever if .sta file is not created or modified


        How to use this workaround:




        1. Create Python file named abq. Code for abq is detailed below. If you are using a solver other than abq2018, replace the line cmd = 'abq20xx.. with the solver that you are using.

        2. Make abq executable and available in your path. I placed abq in the Abaqus commands folder, then ran chmod +x abq

        3. Run an Abaqus standard job by executing abq job=Job-1. This will execute Job-1.inp, then this will kill the standard solver once Job-1.sta is completed.


        Code for abq is below



        #!/usr/bin/python
        import subprocess
        import sys
        import time
        arguments = sys.argv
        jobname = arguments[1].split('job=')[-1]
        cmd = 'abq2018 cpus=4 ask_delete=OFF background job=' + jobname
        p = subprocess.call(cmd, shell=True)

        complete = False
        termination_criteria = [' THE ANALYSIS HAS COMPLETED SUCCESSFULLYn',
        ' THE ANALYSIS HAS NOT BEEN COMPLETEDn']

        while complete is False:
        # wait every 5 seconds
        time.sleep(5)
        try:
        with open(jobname + '.sta', 'r') as f:
        last = f.readlines()[-1]
        if last in termination_criteria:
        # this will kill any process named standard
        subprocess.call('pgrep standard | xargs kill', shell=True)
        complete = True
        except IOError:
        # model.sta has been deleted or doesn't exist
        # try again in 5 seconds
        time.sleep(5)







        share|improve this answer












        share|improve this answer



        share|improve this answer










        answered Jan 22 at 15:27









        Charles JekelCharles Jekel

        1




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