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