Please try the attached patch - and see if it works [without removing IntelMPI from env] you can apply it with 'patch' command from cygwin cd /home/petsc-3.6.4 patch -Np1 < mpich-ver-test.patch Satish On Mon, 6 Feb 2017, Satish Balay wrote:
Thinking about this - configure should not fail with MSMPI even if Intel-MPI is in the default path.
A workarround is [after successful configure] - edit PETSC_ARCH/include/petscconf.h and remove the lines:
#ifndef PETSC_HAVE_MPICH_NUMVERSION #define PETSC_HAVE_MPICH_NUMVERSION 30200300 #endif
And then run 'make all'
Will have to check on the fix..
Satish
On Mon, 6 Feb 2017, Mohammad S Dodaran wrote:
I will remove intel mpi env tomorrow first thing in the morning and then i will send you the log files. Mohammad
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________________________________ From: Satish Balay <[email protected]> Sent: Monday, February 6, 2017 11:34:00 PM To: petsc-dev Cc: Mohammad S Dodaran Subject: Re: [petsc-dev] install petsc on windows 10 with mpi
BTW: Why not use petsc-3.7?
Satish
On Mon, 6 Feb 2017, Satish Balay wrote:
Please send the logs for the case that is supporsed to work - but failed.
without the relavent logs - I have no idea what failed.
Satish
On Mon, 6 Feb 2017, Mohammad S Dodaran wrote:
As i stated in my previous email. " i tried to make with and without intel-mpi ENV . in both cases the error had been changed." And the error didnt have any thing to do with intel_mpi ENV. Do you still want me to remove the intel_ mpi env and send you the log file?
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________________________________ From: Satish Balay <[email protected]> Sent: Monday, February 6, 2017 11:15:19 PM To: petsc-dev Cc: Mohammad S Dodaran Subject: Re: [petsc-dev] install petsc on windows 10 with mpi
never mind.
#line 2416 "c:\\program files (x86)\\intelswtools\\compilers_and_libraries_2017.1.143\\windows\\mpi\\intel64\\include\\mpi.h"^M ^M #line 2418 "c:\\program files (x86)\\intelswtools\\compilers_and_libraries_2017.1.143\\windows\\mpi\\intel64\\include\\mpi.h"^M ^M #line 4 "C:\\cygwin64\\tmp\\PE5639~1\\CONFIG~1.MPI\\conftest.c"^M int mpich_ver = 30200300; Defined "HAVE_MPICH_NUMVERSION" to "30200300" Checking for functions [MPI_Alltoallw] in library ['/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpi.lib', '/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/ms\ mpifec.lib'] [] Pushing language C
<<<<<<<<<<
Its still picking up mpi.h from intel MPI
INCLUDE=C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2017.1.143\windows\compiler\include;C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2017.1.143\windows\compiler\include\intel64;C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\INCLUDE;C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\ATLMFC\INCLUDE;C:\Program Files (x86)\Windows Kits\8.1\include\shared;C:\Program Files (x86)\Windows Kits\8.1\include\um;C:\Program Files (x86)\Windows Kits\8.1\include\winrt;C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2017.1.143\windows\mpi\intel64\bin\..\..\intel64\include;C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2017.1.143\windows\ipp\include;C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2017.1.143\windows\mkl\include;C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2017.1.143\windows\tbb\bin\..\include;C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2017.1.143\windows\daal\include;C:\Program Files (x86)\IntelSWTools\itac_2017\include;C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2017.1.143\windows\mpi\intel64\bin\..\..\intel64\include; <<<<<<<<<<<
The env has "C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2017.1.143\windows\mpi\intel64\bin\..\..\intel64\include" from where mpi.h is getting picked up.
If you can't remove it perhaps you can try using it instead of MSMPI
Satish
On Mon, 6 Feb 2017, Satish Balay wrote:
can you also send make.log?
Satish
On Mon, 6 Feb 2017, Mohammad S Dodaran wrote:
i was trying to repair my parallel_studio_xe_2017. then i configure it once again and then i tried to make with and without intel-mpi ENV . in both cases the error had been changed. i have attached the configure.log
________________________________ From: Satish Balay <[email protected]> Sent: Monday, February 6, 2017 10:10:43 PM To: Mohammad S Dodaran Cc: petsc-dev Subject: Re: [petsc-dev] install petsc on windows 10 with mpi
Them Intel-MPI was not removed. You can resend configure.log to confirm..
Satish
On Mon, 6 Feb 2017, Mohammad S Dodaran wrote:
I removed the INTEL-MPI from the environmental variables and I still have the same problem. When I configure it looks like it accepts the mpi_include and mpi_lib but when I want to build , it says the configure was with mpi but in build it appears to compile is using a non-mpich.
Mohammad
________________________________ From: Satish Balay <[email protected]> Sent: Monday, February 6, 2017 6:13:04 PM To: Mohammad S Dodaran Cc: petsc-dev Subject: Re: [petsc-dev] install petsc on windows 10 with mpi
1. configure.log is a cygwin simlink - so native mail app is unable to attach correctly. The actual file is in PETSC_DIR/PETSC_ARCH/lib/petsc/conf
2. Suggest doing the build without fftw and hdf5 packages [once the basic build succeeds - you can look at adding these pacakges.]
3. remove INTEL-MPI from your env - before running configure. [you might be able to use intel-mpi instead of ms-mpi - but we don't have any experience with it]
Satish
On Mon, 6 Feb 2017, Mohammad S Dodaran wrote:
now I'm trying to configure petsc 3.7 i used the format you showd in your previous email for the directories of fftw and hdf5 as below
--with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5
the result is the following
TESTING: alternateConfigureLibrary from config.packages.glut(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.giflib(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.scientificpython(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.fiat(config/BuildSystem/config/package.py:742) TESTING: configureLibrary from config.packages.fftw(config/BuildSystem/config/package.py:679) ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw did not work *******************************************************************************
i also attached the configure.log
________________________________ From: Satish Balay <[email protected]> Sent: Monday, February 6, 2017 4:28:09 PM To: Mohammad S Dodaran Cc: Matthew Knepley; petsc-dev Subject: Re: [petsc-dev] install petsc on windows 10 with mpi
Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-cc="win32fe cl" --with-fc="win32fe ifort" --with-cxx="win32fe cl" --with-mpi-include="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include/x64]" --with-mpi-lib="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpi.lib,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpifec.lib]" --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" --download-fblaslapack=1 --with-c2html=0 --with-debugging=0 --with-ssl=0 --with-x=0 PETSC_ARCH= PETSC_DIR=/home/petsc-3.6.4 <<<<
'PETSC_ARCH='
Can you rerun with a non-empty PETSC_ARCH string - or let configure choost default..
--with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]"
I don't think I've built these packages with MS compilers before. Somehow they are not picked up anyway. For one - the format here should be the following [but I don't know if that will make configure check for them]:
--with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5
PETSC_DIR=/home/petsc-3.6.4
Also - please use latest petsc-3.7 release.
C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h"
Hm - configure is picking up Intel-MPI from your 'INCLUDE' env variable - but not 'make' - not sure whats hapenning - but I think its best to start a clean build with petsc-3.7 [unless you need 3.6 for a specific need]
Satish
On Mon, 6 Feb 2017, Mohammad S Dodaran wrote:
hello
i configured petsc and i was trying to make then this error appeared
Using mpiexec: mpiexec ========================================== Building PETSc using GNU Make with 4 build threads ========================================== make[2]: Entering directory '/home/petsc-3.6.4' /usr/bin/python ./config/gmakegen.py --petsc-arch=../petsc-3.6.4 Use "/usr/bin/make V=1" to see the verbose compile lines. CC ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o CC ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o CC ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o CC ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o verboseinfo.c C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o] Error 2 make[2]: *** Waiting for unfinished jobs.... verboseinfof.c C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o] Error 2 zverboseinfof.c C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o] Error 2 zsys.c C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o] Error 2 make[2]: Leaving directory '/home/petsc-3.6.4' make[1]: *** [/home/petsc-3.6.4/lib/petsc/conf/rules:107: gnumake] Error 2 make[1]: Leaving directory '/home/petsc-3.6.4' **************************ERROR************************************* Error during compile, check ../petsc-3.6.4/lib/petsc/conf/make.log Send it and ../petsc-3.6.4/lib/petsc/conf/configure.log to [email protected] ******************************************************************** make: *** [makefile:30: all] Error 1
i have also attached the configure.log and make.log
regards Mohammad
________________________________ From: Matthew Knepley <[email protected]> Sent: Monday, February 6, 2017 8:07:41 AM To: Mohammad S Dodaran Cc: petsc-dev Subject: Re: [petsc-dev] install petsc on windows 10 with mpi
On Sun, Feb 5, 2017 at 11:26 PM, Mohammad S Dodaran <[email protected]<mailto:[email protected]>> wrote:
Satish,
Thanks for your quick response. as you see I can ls to the directory:
ls /cygdrive/c/Program\ Files\ \(x86\)/Microsoft\ SDKs/MPI/Include/
Yes, but as Satish said, there are spaces in the path above. We do not allow spaces in the path. You cannot give a path to configure with spaces.
You can remove the spaces using the cygpath command that Satish showed. Please use that command. Remove the spaces from this path and give the spaceless path to configure.
Thanks,
Matt
mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64/ x86/
but I do not know why still it has the same problem. and my configure file looks strange.
Best,
Mohammad
________________________________ From: Satish Balay <[email protected]<mailto:[email protected]>> Sent: Sunday, February 5, 2017 10:58:35 PM To: Mohammad S Dodaran Cc: [email protected]<mailto:[email protected]> Subject: Re: [petsc-dev] install petsc on windows 10 with mpi
Try to figureout path without spaces.
cygpath -u `cygpath -s -m PATH`
Make sure you can do "ls" on this path.
And use it with petsc configure.
balay@ps4 ~ $ cygpath -u `cygpath -s -m /cygdrive/c/Program\ Files\ \(x86\)/Microsoft\ SDKs/MPI/Include` /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include
balay@ps4 ~ $ ls /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64 x86
balay@ps4 ~ $
For ex: - I use:
$ cat config/examples/arch-mswin-intel.py #!/usr/bin/python if __name__ == '__main__': import sys import os sys.path.insert(0, os.path.abspath('config')) import configure configure_options = [ '--download-fblaslapack=1', '--with-cc=win32fe icl', '--with-cxx=win32fe icl', '--with-fc=win32fe ifort', '--with-mpi-include=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/,/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/x64]', '--with-mpi-lib=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpifec.lib,/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpi.lib]', '--with-mpiexec=/cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec', '--with-shared-libraries=0', 'DATAFILESPATH=c:/cygwin64/home/petsc/datafiles', ] configure.petsc_configure(configure_options)
<<<<<<<<<<<
if you still have issues - send us configure.log for the failure.
Satish
On Sun, 5 Feb 2017, Mohammad S Dodaran wrote:
Dear Petsc developers,
I am trying to install Petsc on windows 10 but I have a problem. I installed MS-MPI v8<http://go.microsoft.com/FWLink/p/?LinkID=389556> separately and in the configure options I use
--with-mpi-include="/cygdrive/c/Program\ Files\ \(x86\)/Microsoft\ SDKs/MPI/Include" --with-mpi-lib="/cygdrive/c/Program\ Files\ \(x86\)/Microsoft\ SDKs/MPI/Lib/x64/msmpi.lib"
But it gives error which says:
*************************************************************** ERROR in COMMAND LINE ARGUMENT to ./configure ------------------------------------------------------------------------------- Invalid directory: [/cygdrive/c/Program\ Files\ \(x86\)/Microsoft\ SDKs/MPI/Include for key with-mpi-include
How should I solve it?
Mohammad
-- 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