[gmx-users] orca and Segmentation fault

[Christoph Riplinger]

Dear xi zhao,

In your case GMX is applying threading and thus not only a single QM job 
is requested, but eight. You should run mdrun with -nt 1. Then GMX uses 
only one single CPU and ORCA is called only once (but can be used in 
parallel).
Hope that helps,
Christoph

On 11/14/2011 10:34 AM, xi zhao wrote:
> dear sir :
>  I installed gromacs-orca for qm/mm
> ./configure --without-qmmm-orca --with--qmmm-gaussian --enable-mpi
> make
> make install
> MPI is lam-mpi
> when run mdrun , the error
> " Back Off! I just backed up md.log to ./#md.log.12#
> Getting Loaded...
> Reading file pyp.tpr, VERSION 4.5.1 (single precision)
> Loaded with Money
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> there we go!
> there we go!
> there we go!
> there we go!
> there we go!
> there we go!
> there we go!
> Layer 0
> nr of QM atoms 22
> QMlevel: B3LYP/3-21G
> orca initialised...
> [localhost:17937] *** Process received signal ***
> [localhost:17939] *** Process received signal ***
> [localhost:17937] Signal: Segmentation fault (11)
> [localhost:17937] Signal code: Address not mapped (1)
> [localhost:17937] Failing at address: 0x10
> [localhost:17940] *** Process received signal ***
> [localhost:17939] Signal: Segmentation fault (11)
> [localhost:17939] Signal code: Address not mapped (1)
> [localhost:17939] Failing at address: 0x10
> [localhost:17936] *** Process received signal ***
> [localhost:17936] Signal: Segmentation fault (11)
> [localhost:17936] Signal code: Address not mapped (1)
> [localhost:17936] Failing at address: 0x10
> [localhost:17934] *** Process received signal ***
> [localhost:17938] *** Process received signal ***
> [localhost:17934] Signal: Segmentation fault (11)
> [localhost:17934] Signal code: Address not mapped (1)
> [localhost:17934] Failing at address: 0x10
> [localhost:17940] Signal: Segmentation fault (11)
> [localhost:17940] Signal code: Address not mapped (1)
> [localhost:17940] Failing at address: 0x10
> [localhost:17938] Signal: Segmentation fault (11)
> [localhost:17938] Signal code: Address not mapped (1)
> [localhost:17938] Failing at address: 0x10
> [localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
> [localhost:17939] [ 1] mdrun_dd [0x534a93]
> [localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
> [localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
> [localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619]
> [localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
> [0x35c4f1c3fb]
> [localhost:17939] [ 6] mdrun_dd [0x41bcfa]
> [localhost:17939] *** End of error message ***
> [localhost:17936] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
> [localhost:17936] [ 1] mdrun_dd [0x534a93]
> [localhost:17936] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
> [localhost:17936] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
> [localhost:17936] [ 4] mdrun_dd(main+0xe69) [0x43d619]
> [localhost:17936] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
> [0x35c4f1c3fb]
> [localhost:17936] [ 6] mdrun_dd [0x41bcfa]
> [localhost:17936] *** End of error message ***
> [localhost:17940] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
> [localhost:17940] [ 1] mdrun_dd [0x534a93]
> [localhost:17940] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
> [localhost:17940] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
> [localhost:17940] [ 4] mdrun_dd(main+0xe69) [0x43d619]
> [localhost:17940] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
> [0x35c4f1c3fb]
> [localhost:17940] [ 6] mdrun_dd [0x41bcfa]
> [localhost:17940] *** End of error message ***
> there we go!
> [localhost:17935] *** Process received signal ***
> [localhost:17935] Signal: Segmentation fault (11)
> [localhost:17935] Signal code: Address not mapped (1)
> [localhost:17935] Failing at address: 0x10
> [localhost:17935] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
> [localhost:17935] [ 1] mdrun_dd [0x534a93]
> [localhost:17935] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
> [localhost:17935] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
> [localhost:17935] [ 4] mdrun_dd(main+0xe69) [0x43d619]
> [localhost:17935] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
> [0x35c4f1c3fb]
> [localhost:17935] [ 6] mdrun_dd [0x41bcfa]
> [localhost:17935] *** End of error message ***
> [localhost:17934] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
> [localhost:17934] [ 1] mdrun_dd [0x534a93]
> [localhost:17934] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
> [localhost:17934] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
> [localhost:17934] [ 4] mdrun_dd(main+0xe69) [0x43d619]
> [localhost:17934] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
> [0x35c4f1c3fb]
> [localhost:17934] [ 6] mdrun_dd [0x41bcfa]
> [localhost:17934] *** End of error message ***
> [localhost:17937] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
> [localhost:17937] [ 1] mdrun_dd [0x534a93]
> [localhost:17937] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
> [localhost:17937] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
> [localhost:17937] [ 4] mdrun_dd(main+0xe69) [0x43d619]
> [localhost:17937] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
> [0x35c4f1c3fb]
> [localhost:17937] [ 6] mdrun_dd [0x41bcfa]
> [localhost:17937] *** End of error message ***
> [localhost:17938] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
> [localhost:17938] [ 1] mdrun_dd [0x534a93]
> [localhost:17938] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
> [localhost:17938] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
> [localhost:17938] [ 4] mdrun_dd(main+0xe69) [0x43d619]
> [localhost:17938] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
> [0x35c4f1c3fb]
> [localhost:17938] [ 6] mdrun_dd [0x41bcfa]
> [localhost:17938] *** End of error message ***
> Making 2D domain decomposition 4 x 2 x 1
> --------------------------------------------------------------------------
> mpirun noticed that process rank 3 with PID 17936 on node 
> localhost.localdomai exited on signal 11 (Segmentation fault).
>
>
> 4 
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>

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