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Hi Srinivasu,
<div class=""><br class="">
</div>
<div class="">In the commands you listed, you unload the OpenMPI module, but don’t load any other MPI modules. Are you certain that Intel MPI is available by default? The fact that `make depend` couldn’t find `mpif.h`, makes me suspect that you are trying to
compile against an MPI that isn’t available.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Ed</div>
<div class=""><br class="">
<div class="">
<div style="color: rgb(0, 0, 0); font-family: Palatino; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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<span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px;"><font face="Tahoma" size="2" class=""><span dir="ltr" style="font-size: 10pt;" class=""><font size="1" class=""><span style="font-size: 13px;" class=""><font size="2" class=""><b class="">Edward
Doddridge</b><br class="">
<i class="">Postdoctoral researcher</i></font></span></font></span></font></span></span></div>
<div style="color: rgb(0, 0, 0); font-family: Palatino; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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Atmospheric and Planetary Sciences</i></font></span></font></span></font></span></span></div>
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<span class="Apple-style-span" style="font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; border-collapse: separate; border-spacing: 0px;"><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px;"><font face="Tahoma" size="2" class=""><span dir="ltr" style="font-size: 10pt;" class=""><font size="1" class=""><span style="font-size: 13px;" class=""><font size="2" class=""><i class="">Massachusetts
Institute of Technology</i></font></span></font></span></font></span></span></div>
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</i></font></span></font></span></font></span></span></div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On 11 Sep 2018, at 01:05, Srinivasu U <<a href="mailto:srinivasu.u@incois.gov.in" class="">srinivasu.u@incois.gov.in</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="caret-color: rgb(0, 0, 0); font-size: 12pt; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; background-color: rgb(255, 255, 255); font-family: Arial, Helvetica, sans-serif;" class="">
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div class="">Thank you very much for your follow up response.<br class="">
</div>
<div class="">I tried to compile with all intel-MPI as follows(avoiding openMPI)<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">cd /moes/home/srinivas/MITgcm/verification/tutorial_barotropic_gyre/build<br class="">
</div>
<div class="">module unload netcdf/4.2.1</div>
<div class="">module load netcdf/3.6.3_new</div>
<div class="">module unload openmpi/1.8.4</div>
<div class="">export NETCDF_ROOT="/gpfs1/home/Libs/INTEL/NETCDF-3.6.3_new"</div>
<div class="">export MPI="true"</div>
<div class="">export MPI_INC_DIR="/gpfs1/opt/intel/icsxe/impi/4.1.3.048/intel64"</div>
<div class=""><br class="">
</div>
<div class="">with MPI support and with netcdf support</div>
<div class="">../../../tools/genmake2 -mpi -enable=mnc -mods ../code -optfile ../../../tools/build_options/linux_amd64_ifort+impi <br class="">
</div>
<div class="">make depend<br class="">
</div>
<div class=""><br class="">
</div>
Now at make depend stage itself. I am getting a lot of following errror.<br class="">
</div>
<div class="">EESUPPORT.h:173: error: mpif.h: No such file or directory</div>
<div class="">In file included from bar2.F:24:<br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I attached linux_amd64_ifort+impi for your reference.<br class="">
</div>
<div class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div name="divtagdefaultwrapper" style="font-family: calibri, arial, helvetica, sans-serif; margin: 0px;" class="">
<div class="BodyFragment"><font size="2" class="">
<div class="PlainText"><strong class=""><em class="">Srinivasu U</em></strong><br class="">
<strong class=""><em class="">Scientist-C, CSG,</em></strong><br class="">
<strong class=""><em class="">Indian National Center for Ocean Information Services(INCOIS),</em></strong><br class="">
<strong class=""><em class="">Hyderabad-500090.</em></strong></div>
<div class="PlainText"><strong class=""><em class="">Telephone:04023886146</em></strong><br class="">
<strong class=""><em class="">Mobile:9032325438.</em></strong></div>
</font></div>
</div>
</div>
<div style="color: rgb(40, 40, 40);" class="">
<hr tabindex="-1" style="display: inline-block; width: 1156.390625px;" class="">
<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><strong class=""><em class="">From:</em></strong><strong class=""><em class=""><span class="Apple-converted-space"> </span>MITgcm-support <<a href="mailto:mitgcm-support-bounces@mitgcm.org" class="">mitgcm-support-bounces@mitgcm.org</a>>
on behalf of Ali Ramadhan <<a href="mailto:alir@mit.edu" class="">alir@mit.edu</a>></em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Sent:</em></strong><strong class=""><em class=""><span class="Apple-converted-space"> </span>Friday, September 7, 2018 6:48 PM</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">To:</em></strong><strong class=""><em class=""><span class="Apple-converted-space"> </span><a href="mailto:mitgcm-support@mitgcm.org" class="">mitgcm-support@mitgcm.org</a></em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Subject:</em></strong><strong class=""><em class=""><span class="Apple-converted-space"> </span>Re: [MITgcm-support] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack</em></strong></font><strong class=""></strong>
<div class=""> </div>
</div>
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class=""><strong class=""><em class="">Hi Srinivasu,</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""><em class="">Can you check to see if mpirun, mpiifort, and mpiicc are all coming from the same installation using the which command? Also, can you post your SIZE.h file? The number of processors specified with the -np flag must equal nPx*nPy
from SIZE.h.</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""><em class="">Also I think I just noticed a mistake in your original post. You should be linking to the mitgcmuv executable, not copying it. The commands</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""><em class="">cd ../run</em></strong><br class="">
<strong class=""><em class="">ln -s ../input/* .</em></strong><br class="">
<strong class=""><em class="">cp ../build/mitgcmuv .</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""><em class="">should be</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""><em class="">cd ../run</em></strong><br class="">
<strong class=""><em class="">ln -s ../input/* .</em></strong><br class="">
<strong class=""><em class="">ln -s ../build/mitgcmuv .</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""><em class="">Well, actually it should run fine if you just copy the executable but then if you change some code and recompile/remake you may forget to copy the new executable and run the old executable without realizing it.</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""><em class="">Cheers,</em></strong><br class="">
<strong class=""><em class="">Ali</em></strong><br class="">
<strong class=""></strong></div>
</div>
<strong class=""></strong><br class="">
<strong class=""></strong>
<div class="gmail_quote">
<div dir="ltr" class=""><strong class=""><em class="">On Fri, Sep 7, 2018 at 1:07 AM Srinivasu U <</em></strong><a href="mailto:srinivasu.u@incois.gov.in" class=""><strong class=""><em class="">srinivasu.u@incois.gov.in</em></strong></a><strong class=""><em class="">>
wrote:</em></strong><br class="">
<strong class=""></strong></div>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">
<div class="">
<div style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: arial, helvetica, sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><strong class=""><em class="">Hi Ali,</em></strong><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><strong class=""><em class="">Thanks for your reply. I unloaded openmpi and run "which mpirun". As you said, it is showing a different mpirun path.</em></strong><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><strong class=""><em class="">module load openmpi</em></strong><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><strong class=""><em class="">which mpirun</em></strong><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><strong class=""><em class="">/gpfs1/home/Libs/INTEL/OPENMPI/openmpi-1.8.4/bin/mpirun</em></strong><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><strong class=""><em class="">module unload openmpi</em></strong><br class="">
<strong class=""></strong></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">which mpirun</em></strong><br class="">
<strong class=""></strong></div>
<div class=""><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">/gpfs1/opt/intel/icsxe/impi/</em></strong><a href="http://4.1.3.048/intel64/bin/mpirun" target="_blank" class=""><strong class=""><em class="">4.1.3.048/intel64/bin/mpirun</em></strong></a><br class="">
<strong class=""></strong></div>
<div class=""><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">I tried to run with second mpirun, but getting the same error.</em></strong><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">Same error persists which mpiexec as well.</em></strong><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">Any more suggestions?</em></strong><br class="">
<strong class=""></strong></div>
<div class=""><br class="">
<strong class=""></strong><span style="font-size: small; font-family: calibri, arial, helvetica, sans-serif;" class=""><strong class=""><em class="">Srinivasu U</em></strong></span><br class="">
<strong class=""></strong></div>
<div class="">
<div name="divtagdefaultwrapper" style="font-family: calibri, arial, helvetica, sans-serif; margin: 0px;" class="">
<div class="m_-6815878227422177730BodyFragment"><font size="2" class="">
<div class="m_-6815878227422177730PlainText"><strong class=""><em class="">Scientist-C, CSG,</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Indian National Center for Ocean Information Services(INCOIS),</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Hyderabad-500090.</em></strong></div>
<div class="m_-6815878227422177730PlainText"><strong class=""><em class="">Telephone:04023886146</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Mobile:9032325438.</em></strong></div>
</font></div>
</div>
</div>
<div style="color: rgb(40, 40, 40);" class="">
<hr style="display: inline-block; width: 1140.78125px;" class="">
<div id="m_-6815878227422177730divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><strong class=""><em class="">From:</em></strong><strong class=""><em class=""><span class="Apple-converted-space"> </span>MITgcm-support
<</em></strong><a href="mailto:mitgcm-support-bounces@mitgcm.org" target="_blank" class=""><strong class=""><em class="">mitgcm-support-bounces@mitgcm.org</em></strong></a><strong class=""><em class="">> on behalf of Ali Ramadhan <</em></strong><a href="mailto:alir@mit.edu" target="_blank" class=""><strong class=""><em class="">alir@mit.edu</em></strong></a><strong class=""><em class="">></em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Sent:</em></strong><strong class=""><em class=""><span class="Apple-converted-space"> </span>Thursday, September 6, 2018 6:37 PM</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">To:</em></strong><strong class=""><span class="Apple-converted-space"> </span></strong><a href="mailto:mitgcm-support@mitgcm.org" target="_blank" class=""><strong class=""><em class="">mitgcm-support@mitgcm.org</em></strong></a><br class="">
<strong class=""></strong><strong class=""><em class="">Subject:</em></strong><strong class=""><em class=""><span class="Apple-converted-space"> </span>Re: [MITgcm-support] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack</em></strong></font><strong class=""></strong><strong class=""></strong>
<div class=""> </div>
</div>
<div class="">
<div dir="ltr" class="">
<div class=""><strong class=""><em class="">Hi Srinivas,</em></strong></div>
<div class=""><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">I think I had a similar problem a few weeks ago. I notice you are correctly using the " linux_amd64_ifort+impi" build option which should compile using the mpiifort and mpiicc compilers, but then use mpirun from OpenMPI.</em></strong></div>
<div class=""><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">What worked for me was using the mpirun provided by the intel compiler (impi) which you presumably have loaded for compilation. If you<span class="Apple-converted-space"> </span></em></strong><span style="font-family: monospace, monospace;" class=""><strong class=""><em class="">"module
unload openmpi"</em></strong></span><strong class=""><em class=""><span class="Apple-converted-space"> </span>do you still have an mpirun in your PATH? You can run<span class="Apple-converted-space"> </span></em></strong><span style="font-family: monospace, monospace;" class=""><strong class=""><em class="">"which
mpirun"</em></strong></span><strong class=""><em class=""><span class="Apple-converted-space"> </span>to check</em></strong><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class=""> where it is located, hopefully from the Intel compiler.</em></strong></div>
<div class=""><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">I should also mention that Intel's mpirun and mpiexec are slightly different so if mpirun still does not work, maybe try mpiexec.</em></strong></div>
<div class=""><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">Let us know if this helps or not!</em></strong><br class="">
<strong class=""></strong></div>
<div class=""><br class="">
<strong class=""></strong></div>
<div class=""><strong class=""><em class="">Cheers,</em></strong></div>
<div class=""><strong class=""><em class="">Ali</em></strong><br class="">
<strong class=""></strong></div>
</div>
<strong class=""></strong><br class="">
<strong class=""></strong><strong class=""></strong>
<div class="gmail_quote">
<div dir="ltr" class=""><strong class=""><em class="">On Thu, Sep 6, 2018 at 6:23 AM Srinivasu U <</em></strong><a href="mailto:srinivasu.u@incois.gov.in" target="_blank" class=""><strong class=""><em class="">srinivasu.u@incois.gov.in</em></strong></a><strong class=""><em class="">>
wrote:</em></strong><br class="">
<strong class=""></strong></div>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">
<strong class=""></strong><strong class=""><em class="">Dear MITgcm support,</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""></strong><strong class=""><em class="">I am trying to run a tutorial example of tutorial_barotropic_gyre</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""></strong><strong class=""><em class="">I built it as follows</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""></strong><strong class=""><em class="">cd verification/tutorial_barotropic_gyre/build</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">module unload netcdf/4.2.1</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">module load netcdf/3.6.3_new</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">module load openmpi/1.8.4</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">export NETCDF_ROOT=”/gpfs1/home/Libs/INTEL/NETCDF-3.6.3_new”</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">export MPI_INC_DIR="/gpfs1/home/Libs/INTEL/OPENMPI/openmpi-1.8.4/include”</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">../../../tools/genmake2 -enable=mnc -mods ../code -optfile ../../../tools/build_options/linux_amd64_ifort+impi -mpi</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">make depend</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">make</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""></strong><strong class=""><em class="">cd ../run</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">ln -s ../input/* .</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">cp ../build/mitgcmuv .</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""></strong><strong class=""><em class="">But while running the model as follows</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">mpirun -np 4 ./mitgcmuv</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">I get the following error</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">PMPI_Comm_rank(121): MPI_Comm_rank(comm=0x0, rank=0xeea1a4) failed</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">PMPI_Comm_rank(73).: Invalid communicator</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Thanks in Advance.</em></strong><br class="">
<strong class=""></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Srinivasu U</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Scientist-C, CSG,</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Indian National Center for Ocean Information Services(INCOIS),</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Hyderabad-500090.</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Telephone:04023886146</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">Mobile:9032325438.</em></strong><br class="">
<strong class=""></strong><strong class=""><em class="">_______________________________________________</em></strong><br class="">
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<strong class=""></strong><a href="mailto:MITgcm-support@mitgcm.org" target="_blank" class=""><strong class=""><em class="">MITgcm-support@mitgcm.org</em></strong></a><br class="">
<strong class=""></strong><a href="http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support" rel="noreferrer" target="_blank" class=""><strong class=""><em class="">http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</em></strong></a><br class="">
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