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
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