[gmx-users] Gromacs 2016.3 FLOATING-POINT EXECPTION/DIVIDE-BY_ZERO errors
HI!.
My name is Rainer. I am one of the module-/SW-maintainers
for the bwHPC-C5-project. "http://www.bwhpc-c5.de/en/index.php";
Since a couple of time we can't run Gromacs 2016.n on
our clusters. Here's one of the errors we received from
one of the users:
I am using Gromacs on BwUniCluster for few months and I performed
molecular Dynamics Simulations without any problem until the end of
July. Since August, I cannot prepare the input file and if I prepare
them elsewhere, the simulation crash although it was the same that the
ones which perfectly worked few days before. It seems that I have not
such problem smaller systems with less atoms.
uc1n997:43275] *** Process received signal ***
[uc1n997:43275] Signal: Floating point exception (8)
[uc1n997:43275] Signal code: Integer divide-by-zero (1)
[uc1n997:43275] Failing at address: 0x42fd74
[uc1n997:43275] [ 0] /usr/lib64/libpthread.so.0(+0xf5e0)[0x2b65e89805e0]
[uc1n997:43275] [ 1] gmx_mpi_d(__svml_idiv4_h9+0x64)[0x42fd74]
[uc1n997:43275] [ 2]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(count_bonded_distances+0x43c)[0x2b65e6b1f72c]
[uc1n997:43275] [ 3]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(pme_load_estimate+0x20)[0x2b65e6b1ef70]
[uc1n997:43275] [ 4]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(gmx_grompp+0x257a)[0x2b65e639e84a]
[uc1n997:43275] [ 5]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x267)[0x2b65e6127e97]
[uc1n997:43275] [ 6] gmx_mpi_d(main+0xbc)[0x40c13c]
[uc1n997:43275] [ 7]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b65e8baec05]
[uc1n997:43275] [ 8] gmx_mpi_d[0x40bfb9]
[uc1n997:43275] *** End of error message ***
Gromacs 2016.3 was build this way (excerpt):
[...]
# #(3) Load required modules for build process
module load compiler/intel/16.0
module load mpi/openmpi/2.1-intel-16.0
module load numlib/mkl/11.3.4
module load devel/cmake/3.3.2
[...]
# double precission
cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DGMX_MPI=ON -DGMX_GPU=OFF
-DGMX_DOUBLE=ON -DGMX_THREAD_MPI=OFF -DGMX_FFT_LIBRARY=mkl
-DMPIEXEC=${MPI_BIN_DIR}/mpirun -DREGRESSIONTEST_DOWNLOAD=OFF
-DCMAKE_INSTALL_PREFIX=${TARGET_DIR}
make 2>&1 | tee ${LOG_DIR}/make_double.out
make install 2>&1 | tee ${LOG_DIR}/make-install_double.out
[...]
ANY HELP IS MUCH APPRECIATED.
Thanx in advance.
.-)
--
Rainer Rutka
University of Konstanz
Communication, Information, Media Centre (KIM)
* High-Performance-Computing (HPC)
* KIM-Support and -Base-Services
Room: V511
78457 Konstanz, Germany
+49 7531 88-5413
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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[gmx-users] Gromacs 2016.3 FLOATING-POINT EXECPTION/DIVIDE-BY_ZERO errors
HI!.
My name is Rainer. I am one of the module-/SW-maintainers
for the bwHPC-C5-project. "http://www.bwhpc-c5.de/en/index.php";
Since a couple of time we can't run Gromacs 2016.n on
our clusters. Here's one of the errors we received from
one of the users:
I am using Gromacs on BwUniCluster for few months and I performed
molecular Dynamics Simulations without any problem until the end of
July. Since August, I cannot prepare the input file and if I prepare
them elsewhere, the simulation crash although it was the same that the
ones which perfectly worked few days before. It seems that I have not
such problem smaller systems with less atoms.
uc1n997:43275] *** Process received signal ***
[uc1n997:43275] Signal: Floating point exception (8)
[uc1n997:43275] Signal code: Integer divide-by-zero (1)
[uc1n997:43275] Failing at address: 0x42fd74
[uc1n997:43275] [ 0] /usr/lib64/libpthread.so.0(+0xf5e0)[0x2b65e89805e0]
[uc1n997:43275] [ 1] gmx_mpi_d(__svml_idiv4_h9+0x64)[0x42fd74]
[uc1n997:43275] [ 2]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(count_bonded_distances+0x43c)[0x2b65e6b1f72c]
[uc1n997:43275] [ 3]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(pme_load_estimate+0x20)[0x2b65e6b1ef70]
[uc1n997:43275] [ 4]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(gmx_grompp+0x257a)[0x2b65e639e84a]
[uc1n997:43275] [ 5]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x267)[0x2b65e6127e97]
[uc1n997:43275] [ 6] gmx_mpi_d(main+0xbc)[0x40c13c]
[uc1n997:43275] [ 7]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b65e8baec05]
[uc1n997:43275] [ 8] gmx_mpi_d[0x40bfb9]
[uc1n997:43275] *** End of error message ***
Gromacs 2016.3 was build this way (excerpt):
[...]
# #(3) Load required modules for build process
module load compiler/intel/16.0
module load mpi/openmpi/2.1-intel-16.0
module load numlib/mkl/11.3.4
module load devel/cmake/3.3.2
[...]
# double precission
cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DGMX_MPI=ON -DGMX_GPU=OFF
-DGMX_DOUBLE=ON -DGMX_THREAD_MPI=OFF -DGMX_FFT_LIBRARY=mkl
-DMPIEXEC=${MPI_BIN_DIR}/mpirun -DREGRESSIONTEST_DOWNLOAD=OFF
-DCMAKE_INSTALL_PREFIX=${TARGET_DIR}
make 2>&1 | tee ${LOG_DIR}/make_double.out
make install 2>&1 | tee ${LOG_DIR}/make-install_double.out
[...]
ANY HELP IS MUCH APPRECIATED.
Thanx in advance.
.-)
--
Rainer Rutka
University of Konstanz
Communication, Information, Media Centre (KIM)
* High-Performance-Computing (HPC)
* KIM-Support and -Base-Services
Room: V511
78457 Konstanz, Germany
+49 7531 88-5413
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs 2016.3 FLOATING-POINT EXECPTION/DIVIDE-BY_ZERO errors
On 05/09/17 11:54, Rainer Rutka wrote:
HI!.
My name is Rainer. I am one of the module-/SW-maintainers
for the bwHPC-C5-project. "http://www.bwhpc-c5.de/en/index.php";
Since a couple of time we can't run Gromacs 2016.n on
our clusters. Here's one of the errors we received from
one of the users:
I am using Gromacs on BwUniCluster for few months and I performed
molecular Dynamics Simulations without any problem until the end of
July. Since August, I cannot prepare the input file and if I prepare
them elsewhere, the simulation crash although it was the same that the
ones which perfectly worked few days before. It seems that I have not
such problem smaller systems with less atoms.
uc1n997:43275] *** Process received signal ***
[uc1n997:43275] Signal: Floating point exception (8)
[uc1n997:43275] Signal code: Integer divide-by-zero (1)
[uc1n997:43275] Failing at address: 0x42fd74
[uc1n997:43275] [ 0] /usr/lib64/libpthread.so.0(+0xf5e0)[0x2b65e89805e0]
[uc1n997:43275] [ 1] gmx_mpi_d(__svml_idiv4_h9+0x64)[0x42fd74]
[uc1n997:43275] [ 2]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(count_bonded_distances+0x43c)[0x2b65e6b1f72c]
[uc1n997:43275] [ 3]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(pme_load_estimate+0x20)[0x2b65e6b1ef70]
[uc1n997:43275] [ 4]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(gmx_grompp+0x257a)[0x2b65e639e84a]
[uc1n997:43275] [ 5]
/pfs/data1/software_uc1/bwhpc/common/chem/gromacs/5.1.2-openmpi-1.8-intel-15.0/bin/../lib64/libgromacs_mpi_d.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x267)[0x2b65e6127e97]
[uc1n997:43275] [ 6] gmx_mpi_d(main+0xbc)[0x40c13c]
[uc1n997:43275] [ 7]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b65e8baec05]
[uc1n997:43275] [ 8] gmx_mpi_d[0x40bfb9]
[uc1n997:43275] *** End of error message ***
Gromacs 2016.3 was build this way (excerpt):
[...]
# #(3) Load required modules for build process
module load compiler/intel/16.0
module load mpi/openmpi/2.1-intel-16.0
module load numlib/mkl/11.3.4
module load devel/cmake/3.3.2
[...]
# double precission
cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DGMX_MPI=ON -DGMX_GPU=OFF
-DGMX_DOUBLE=ON -DGMX_THREAD_MPI=OFF -DGMX_FFT_LIBRARY=mkl
-DMPIEXEC=${MPI_BIN_DIR}/mpirun -DREGRESSIONTEST_DOWNLOAD=OFF
-DCMAKE_INSTALL_PREFIX=${TARGET_DIR}
make 2>&1 | tee ${LOG_DIR}/make_double.out
make install 2>&1 | tee ${LOG_DIR}/make-install_double.out
[...]
ANY HELP IS MUCH APPRECIATED.
Much more information is needed than this.
If this system used to work but now it does not anymore than please have
the user submit a bug report at
http://redmine.gromacs.org
Thanx in advance.
.-)
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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