There's a bin64 symlink: $ ls -l /opt/intel/compilers_and_libraries_2017.1.132/linux/mpi total 0 drwxr-xr-x. 3 root root 16 Mar 28 2017 benchmarks lrwxrwxrwx. 1 root root 11 Mar 28 2017 bin64 -> intel64/bin drwxr-xr-x. 2 root root 41 Mar 28 2017 binding lrwxrwxrwx. 1 root root 11 Mar 28 2017 etc64 -> intel64/etc lrwxrwxrwx. 1 root root 15 Mar 28 2017 include64 -> intel64/include drwxr-xr-x. 6 root root 50 Mar 28 2017 intel64 lrwxrwxrwx. 1 root root 11 Mar 28 2017 lib64 -> intel64/lib drwxr-xr-x. 4 root root 28 Mar 28 2017 man drwxr-xr-x. 6 root root 50 Mar 28 2017 mic drwxr-xr-x. 2 root root 78 Mar 28 2017 test $
dr. ir. Christiaan Klaij | Senior Researcher | Research & Development MARIN | T +31 317 49 33 44 | mailto:c.kl...@marin.nl | http://www.marin.nl MARIN news: http://www.marin.nl/web/News/News-items/SSSRIMARIN-seminar-May-18-2018-Shanghai.htm ________________________________________ From: Klaij, Christiaan Sent: Thursday, March 22, 2018 2:43 PM To: petsc-users Subject: Re: [petsc-users] problem configuring 3.8.3 with intel mpi OK, configure works with the option --with-cc=/path/to/mpicc, thanks! I'm not sure you are right about checking --with-mpi-dir/bin, because, at least with this install, the binaries are located in --with-mpi-dir/intel64/bin: $ which mpicc /opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/bin/mpicc Perhaps something to do with intel supporting both 32 and 64bit. Anyway, our sysadmin didn't change any of these locations, they just run the intel installer and this is what we got. ________________________________________ From: Satish Balay <ba...@mcs.anl.gov> Sent: Thursday, March 22, 2018 2:18 PM To: petsc-users Cc: Klaij, Christiaan Subject: Re: [petsc-users] problem configuring 3.8.3 with intel mpi Added this change to balay/mpi-dir-check-warning/maint and merged to next. Satish On Thu, 22 Mar 2018, Satish Balay wrote: > The relevant change that is causing the difference is: > > https://bitbucket.org/petsc/petsc/commits/a98758b74fbc47f3dca87b526141d347301fd5eb > > Perhaps we should print a warning if with-mpi-dir/bin is missing. > > $ ./configure --with-mpi-dir=$HOME/tmp > =============================================================================== > Configuring PETSc to compile on your system > =============================================================================== > =============================================================================== > > ***** WARNING: /home/balay/tmp/bin dir does not exist! > > Skipping check for MPI compilers due to potentially incorrect --with-mpi-dir > option. Suggest > using --with-cc=/path/to/mpicc option instead ****** > > =============================================================================== > > Satish > > --------- > > $ git diff > diff --git a/config/BuildSystem/config/setCompilers.py > b/config/BuildSystem/config/setCompilers.py > index 3b4b723e71..1ca92d309a 100644 > --- a/config/BuildSystem/config/setCompilers.py > +++ b/config/BuildSystem/config/setCompilers.py > @@ -515,6 +515,8 @@ class Configure(config.base.Configure): > if self.useMPICompilers() and 'with-mpi-dir' in self.argDB: > # if it gets here these means that self.argDB['with-mpi-dir']/bin does > not exist so we should not search for MPI compilers > # that is we are turning off the self.useMPICompilers() > + self.logPrintBox('***** WARNING: > '+os.path.join(self.argDB['with-mpi-dir'], 'bin')+ ' dir does not exist!\n > Skipping check for MPI compilers due to potentially incorrect --with-mpi-dir > option.\n Suggest using --with-cc=/path/to/mpicc option instead ******') > + > self.argDB['with-mpi-compilers'] = 0 > if self.useMPICompilers(): > self.usedMPICompilers = 1 > > > On Thu, 22 Mar 2018, Satish Balay wrote: > > > In either case > > --mpi-dir=/opt/intel/compilers_and_libraries_2017.1.132/linux/mpi is the > > wrong option. > > > > Its a shortcut for > > --with-cc=/opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/bin/mpicc > > - which you > > don't have. > > > > Since you have mpicc in your path - you can just use: > > > > --with-cc=mpicc [or skip specifying it - and configure will look at your > > path] > > > > Satish > > > > On Thu, 22 Mar 2018, Klaij, Christiaan wrote: > > > > > Matt, > > > > > > The problem must be earlier, because it should be using mpicc for > > > the check, not gcc. The mpi.h is found here by the 3.7.5 config: > > > > > > Executing: mpicc -E -I/tmp/petsc-JIF0WC/config.setCompilers > > > -I/tmp/petsc-JIF0WC/config.types -I/tmp/petsc-JIF0WC/config.headers > > > -I/opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/include > > > -I/opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/include > > > /tmp/petsc-JIF0WC/config.headers/conftest.c > > > stdout: > > > # 1 "/tmp/petsc-JIF0WC/config.headers/conftest.c" > > > # 1 "/tmp/petsc-JIF0WC/config.headers/confdefs.h" 1 > > > # 2 "/tmp/petsc-JIF0WC/config.headers/conftest.c" 2 > > > # 1 "/tmp/petsc-JIF0WC/config.headers/conffix.h" 1 > > > # 3 "/tmp/petsc-JIF0WC/config.headers/conftest.c" 2 > > > # 1 > > > "/opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/include/mpi.h" > > > 1 > > > > > > Note that the machine and ENV are exactly the same, the only > > > change is 3.7.5 versus 3.8.3. > > > > > > Chris > > > > > > dr. ir. Christiaan Klaij | Senior Researcher | Research & Development > > > MARIN | T +31 317 49 33 44 | c.kl...@marin.nl<mailto:c.kl...@marin.nl> | > > > www.marin.nl<http://www.marin.nl> > > > > > > [LinkedIn]<https://www.linkedin.com/company/marin> [YouTube] > > > <http://www.youtube.com/marinmultimedia> [Twitter] > > > <https://twitter.com/MARIN_nieuws> [Facebook] > > > <https://www.facebook.com/marin.wageningen> > > > MARIN news: Office tool aNySIM integrated into real-time onboard > > > software<http://www.marin.nl/web/News/News-items/Office-tool-aNySIM-integrated-into-realtime-onboard-software-1.htm> > > > > > > ________________________________ > > > From: Matthew Knepley <knep...@gmail.com> > > > Sent: Thursday, March 22, 2018 1:27 PM > > > To: Klaij, Christiaan > > > Cc: petsc-users@mcs.anl.gov > > > Subject: Re: [petsc-users] problem configuring 3.8.3 with intel mpi > > > > > > On Thu, Mar 22, 2018 at 8:00 AM, Klaij, Christiaan > > > <c.kl...@marin.nl<mailto:c.kl...@marin.nl>> wrote: > > > Satish, > > > > > > I'm trying to upgrade from 3.7.5 to 3.8.3. The first problem is > > > that my intel mpi installation, which works for 3.7.5, fails with > > > 3.8.3, see the attached logs. It seems that the mpi compilers are > > > not found anymore. Any ideas? > > > > > > The header check failed: > > > > > > Checking include with compiler flags var CPPFLAGS > > > ['/opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/include'] > > > Executing: gcc -E -I/tmp/petsc-8GlPlN/config.setCompilers > > > -I/tmp/petsc-8GlPlN/config.types -I/tmp/petsc-8GlPlN/config.headers > > > -I/opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/include > > > /tmp/petsc-8GlPlN/config.headers/conftest.c > > > stdout: > > > # 1 "/tmp/petsc-8GlPlN/config.headers/conftest.c" > > > # 1 "<built-in>" > > > # 1 "<command-line>" > > > # 1 "/usr/include/stdc-predef.h" 1 3 4 > > > # 1 "<command-line>" 2 > > > # 1 "/tmp/petsc-8GlPlN/config.headers/conftest.c" > > > # 1 "/tmp/petsc-8GlPlN/config.headers/confdefs.h" 1 > > > # 2 "/tmp/petsc-8GlPlN/config.headers/conftest.c" 2 > > > # 1 "/tmp/petsc-8GlPlN/config.headers/conffix.h" 1 > > > # 3 "/tmp/petsc-8GlPlN/config.headers/conftest.c" 2 > > > Possible ERROR while running preprocessor: exit code 256 > > > stdout: > > > # 1 "/tmp/petsc-8GlPlN/config.headers/conftest.c" > > > # 1 "<built-in>" > > > # 1 "<command-line>" > > > # 1 "/usr/include/stdc-predef.h" 1 3 4 > > > # 1 "<command-line>" 2 > > > # 1 "/tmp/petsc-8GlPlN/config.headers/conftest.c" > > > # 1 "/tmp/petsc-8GlPlN/config.headers/confdefs.h" 1 > > > # 2 "/tmp/petsc-8GlPlN/config.headers/conftest.c" 2 > > > # 1 "/tmp/petsc-8GlPlN/config.headers/conffix.h" 1 > > > # 3 "/tmp/petsc-8GlPlN/config.headers/conftest.c" 2stderr: > > > /tmp/petsc-8GlPlN/config.headers/conftest.c:3:17: fatal error: mpi.h: No > > > such file or directory > > > #include <mpi.h> > > > ^ > > > compilation terminated. > > > Source: > > > #include "confdefs.h" > > > #include "conffix.h" > > > #include <mpi.h> > > > Preprocess stderr before > > > filtering:/tmp/petsc-8GlPlN/config.headers/conftest.c:3:17: fatal error: > > > mpi.h: No such file or directory > > > #include <mpi.h> > > > > > > Where are the headers? > > > > > > Thanks, > > > > > > Matt > > > > > > Chris > > > > > > > > > dr. ir. Christiaan Klaij | Senior Researcher | Research & Development > > > MARIN | T +31 317 49 33 44 | > > > mailto:c.kl...@marin.nl<mailto:c.kl...@marin.nl> | http://www.marin.nl > > > > > > MARIN news: > > > http://www.marin.nl/web/News/News-items/Office-tool-aNySIM-integrated-into-realtime-onboard-software-1.htm > > > > > > > > > > > > > > > -- > > > What most experimenters take for granted before they begin their > > > experiments is infinitely more interesting than any results to which > > > their experiments lead. > > > -- Norbert Wiener > > > > > > https://www.cse.buffalo.edu/~knepley/<http://www.caam.rice.edu/~mk51/> > > > > > > > > > > > > > > >