Hello Dave,
I thought it was something like that.
The error is harmless (just telling you that MPI is doing its job), and
the testing script gets confused because of the extra message in the
output file.
So I think you are good to go (and we need to do something about the
testing script).
Happy simulating!
Cheers
Paul
On 23/10/2019 13:39, Dave M wrote:
Hi Paul,
I checked using this command for a specific folder, and I used '-mpirun
mdrun' rather '-mpirun mpirun':
./gmxtest.pl -mpirun mdrun -np 2 -noverbose rotation
I get lot of these errors:
topol.tpr file different from ./reference_s.tpr. Check files in flex for
flex
FAILED. Check checktpr.out, checktpr.err file(s) in flex for flex
topol.tpr file different from ./reference_s.tpr. Check files in flex-t for
flex-t
FAILED. Check checktpr.out, checktpr.err file(s) in flex-t for flex-t
topol.tpr file different from ./reference_s.tpr. Check files in flex2 for
flex2
FAILED. Check checktpr.out, checktpr.err file(s) in flex2 for flex2
topol.tpr file different from ./reference_s.tpr. Check files in flex2-t for
flex2-t
FAILED. Check checktpr.out, checktpr.err file(s) in flex2-t for flex2-t
.... so on
A) the only suspicious thing I see in checktpr.err is possibly different
software versions.
Command line:
gmx_mpi check -s1 ./reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol
0.001
Note: When comparing run input files, default tolerances are reduced.
Reading file ./reference_s.tpr, VERSION 5.0-beta2-dev-20140130-02adca5
(single precision)
Note: file tpx version 96, software tpx version 116
Reading file topol.tpr, VERSION 2019.4 (single precision)
B) And Only suspicious thing I see in checktpr.out is pasted below (I have
removed the host ip number). Just to mention I use Amazon web services so
probably the following error is related to instance when it was created and
then stored as an image and then re-used with a different ip. May be am
just talking silly!
[[2115,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: ip-xxx-xx-xx-xxx
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
On Wed, Oct 23, 2019 at 4:10 AM Paul bauer <paul.baue...@gmail.com> wrote:
Hello Dave,
this is weird, no idea why it didn't work then.
You can try running the test suite manually in the folder you found with
perl gmxtest.pl -mpirun mpirun -np X -noverbose
That will show if the test binary works and should report any failing
tests.
Don't forget to source the GMXRC file before trying, though!
Cheers
Paul
On 23/10/2019 12:36, Dave M wrote:
Hi Paul,
Thanks for the 'mpirun -n X gmx_mpi mdrun'. It works now.
Regarding tests, I found the folder here build/tests/regressiontests
So I checked all the log using a simple script (searching keyword
'Finished') and it shows that all the log files have Finished properly
in
their corresponding folders. So log files do not say anything here.
On Wed, Oct 23, 2019 at 3:07 AM Paul Bauer <paul.baue...@gmail.com>
wrote:
Hello Dave,
You need to use mpirun -n (number of processes) gmx_mpi mdrun to use a
MPI
enabled build of GROMACS. This is what the error message tries to tell
you,
but we might need to improve on this.
There should be a regressiontests folder somewhere in your build tree
if it
downloaded the tests correctly.
Cheers
Paul
On Wed, 23 Oct 2019, 12:02 Dave M, <dave.gro...@gmail.com> wrote:
Hi Paul,
Thanks for your reply.
a) I just checked there is no tests/regressiontests, some other folder
is
there test/sphysicalvalidation
There is no log file.
b) Regarding thread-mpi I think it is not installed because when I use
some
command like this:
gmx_mpi mdrun -v -deffnm 03-run -rdd 2.0 -nt 2
I get an error:
Fatal error:
Setting the total number of threads is only supported with thread-MPI
and
GROMACS was compiled without thread-MPI
I think (please correct me) gmx_mpi is for external MPI openMPI in my
case
so I tried just 'gmx mdrun' (not gmx_mpi) but then it says command not
found. I am not sure what I missed in installation cmake flags.
Dave
On Wed, Oct 23, 2019 at 2:45 AM Paul Bauer <paul.baue...@gmail.com>
wrote:
Hello Dave,
Did you have a look into the log files from the regression tests under
tests/regressiontests?
They might give us some insight into what is happening.
The warning in respect to thread-MPI is harmless, it just tells you
that
you are using real MPI instead of thread-MPI.
Cheers
Paul
On Wed, 23 Oct 2019, 07:36 Dave M, <dave.gro...@gmail.com> wrote:
Hi All,
Any hints/help much appreciated why am getting regression tests
failure.
Also to mention I think thread-mpi was not installed as I got an
error
saying "MPI is not compatible with thread-MPI. Disabling thread-MPI".
How
to check the compatibility?
Thanks.
best regards,
D
On Sun, Oct 20, 2019 at 2:58 AM Dave M <dave.gro...@gmail.com>
wrote:
Hi All,
I am trying to install gromacs2019.4 with:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=on
-DGMX_MPI=on -DGMX_GPU=on
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs2019_4
-DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug
But 5 tests (41 to 46) were failed copied below:
The following tests FAILED:
41 - regressiontests/simple (Failed)
42 - regressiontests/complex (Failed)
43 - regressiontests/kernel (Failed)
44 - regressiontests/freeenergy (Failed)
45 - regressiontests/rotation (Failed)
Errors while running CTest
CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
'CMakeFiles/run-ctest-nophys' failed
make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
CMakeFiles/Makefile2:1392: recipe for target
'CMakeFiles/run-ctest-nophys.dir/all' failed
make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
CMakeFiles/Makefile2:1172: recipe for target
'CMakeFiles/check.dir/rule'
failed
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
Makefile:626: recipe for target 'check' failed
make: *** [check] Error 2
Not sure what could be wrong. Just to add I get some error/warning
during
installation which says "MPI is not compatible with thread-MPI.
Disabling
thread-MPI". I am using -DGMX_MPI=on and to have openMPI on ubuntu
18.04
I
used "sudo apt-get install openmpi-bin openmpi-common
libopenmpi-dev"
Please let me know how I can fix this.
best regards,
D
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