From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Aug 17 2018 - 13:15:46 CDT
Hi Charlie,
Is the file in NAMD's current directory? I've gotten this when pulling different elements from the configuration file from different places and not adequately taking directory structures into account and telling NAMD to look in the wrong place for something. The current directory is reported in an info line that looks like:
"Info: Working in the current directory /path/to/directory"
-Josh
On 2018-08-16 19:50:42-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
Hi NAMD users,
I am working on submitting a NAMD job remotely on a computing network. I have submitted the job no problem from one directory, but am unable to submit in a neighboring directory.
My process creates a .conf file using VMD, and then inputs it to NAMD. Specifically the error messages I get:
----------------------(everything is fine until here)
Info) Exiting normally.
[hpc-login2:10135] mca: base: component_find: unable to open /usr/usc/openmpi/1.8.4/lib/openmpi/mca_plm_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
[hpc-login2:10135] mca: base: component_find: unable to open /usr/usc/openmpi/1.8.4/lib/openmpi/mca_ras_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
[hpc-login2:10135] 58 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
[hpc-login2:10135] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[hpc-login2:10135] 17 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
[hpc-login2:10135] 11 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
[hpc-login2:10135] 15 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
[hpc-login2:10135] 18 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unable to access config file temp14.conf
[hpc-login2:10135] 98 more processes have sent help message help-mpi-api.txt / mpi-abort
submit pulling 14-th, pid=
---------------------(end error message)
There are a lot of mpi errors, none of which I got from the other directory, but I get them every time here for some reason, even though I am sourcing the same mpi installation.
I checked the file permissions, and they are identical to the temp14.conf file from the adjacent directory, so I have no idea why the program would be unable to access it. I read the file as well, and it doesn't seem to be corrupted.
Any ideas?
Thanks,
Charlie Hoying
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