It seems there is a problem with MPI module file (mpi.mod).
Can you try compiling with a different version?
Best,
Masoud
________________________________
From: Yasser Almeida via AMBER <amber.ambermd.org>
Sent: Tuesday, October 29, 2024 06:25
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] AMBER24 compilation - MPI Fortran
I made a mistake in the cmake with -DMPI=MPI. I change it to -DMPI=TRUE.
Now MPI is recognized in the Features, but still I get the same
compilation error.
Y.
On 29.10.24 11:17, Yasser Almeida via AMBER wrote:
> Hi Masoud,
>
>
> Thank you for your reply.
>
>
> I checked the version of the MPI compilers and gcc and got this:
>
>
> (base) [myasalme.login build]$ mpif90 --version
> GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
>
> (base) [myasalme.login build]$ mpicc --version
> gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
>
> (base) [myasalme.login build]$ gcc --version
> gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
>
>
> Do this means that all these use the same gcc compiler?
>
>
> I first compile the serial version and everything went well. Then, to
> compile the MPI version, I run run_cmake as:
>
>
> cmake $AMBER_PREFIX/amber24_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_BIN \
> -DCOMPILER=GNU \
> -DMPI=MPI -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE \
> 2>&1 | tee cmake.log
>
>
> At the end of the run_cmake I get this:
>
> -- Features:
> -- MPI: OFF
> -- MVAPICH2-GDR for GPU-GPU comm.: OFF
> -- OpenMP: OFF
> -- CUDA: OFF
> -- Build Shared Libraries: ON
> -- Build GUI Interfaces: ON
> -- Build Python Programs: ON
> -- -Python Interpreter: Internal Miniconda (version 3.12)
> -- Build Perl Programs: ON
> -- Build configuration: RELEASE
> -- Target Processor: x86_64
> -- Build Documentation: ON
> -- Sander Variants: normal LES API LES-API MPI
> LES-MPI QUICK-MPI
> -- Install location: /home/myasalme/Softwares/AMBER/amber24_bin/
> -- Installation of Tests: ON
>
>
> For some reason it cannot see the MPI compiler yet and I get the same
> error:
>
> [ 39%] Building Fortran object
> AmberTools/src/quick/src/CMakeFiles/libquick_mpi.dir/modules/quick_mpi_module.f90.o
> f951: Fatal Error: Reading module
> ‘/cluster/intel/2020.1/compilers_and_libraries_2020.1.217/linux/mpi/intel64/include/mpi.mod’
> at line 1 column 2: Unexpected EOF
> compilation terminated.
> make[2]: ***
> [AmberTools/src/quick/src/CMakeFiles/libquick_mpi.dir/build.make:75:
> AmberTools/src/quick/src/CMakeFiles/libquick_mpi.dir/modules/quick_mpi_module.f90.o]
> Error 1
> make[1]: *** [CMakeFiles/Makefile2:8490:
> AmberTools/src/quick/src/CMakeFiles/libquick_mpi.dir/all] Error 2
> make: *** [Makefile:156: all] Error 2
>
>
> Any help is appreciated.
>
>
>
> On 21.10.24 18:35, Masoud Keramati wrote:
> Hi Yasser,
>
> It seems you need to use the same version of gcc that was used to
> compile OpenMPI to compile AMBER24.
>
>
> Best,
>
> Masoud
>
> ________________________________
> From: Yasser Almeida via AMBER
> <amber.ambermd.org><mailto:amber.ambermd.org>
> Sent: Monday, October 21, 2024 10:35
> To: amber.ambermd.org<mailto:amber.ambermd.org>
> <amber.ambermd.org><mailto:amber.ambermd.org>
> Subject: [AMBER] AMBER24 compilation - MPI Fortran
>
> Hello,
>
> I am trying to compile AMBER24 and I am having this error
>
> [ 29%] Building Fortran object
> AmberTools/src/quick/src/CMakeFiles/libquick_mpi.dir/modules/quick_mpi_module.f90.o
> /home/myasalme/Softwares/AMBER/amber24_src/AmberTools/src/quick/src/modules/quick_mpi_module.f90:25:9:
>
>
> 25 | use mpi
> | 1
> Fatal Error: Cannot read module file
> ‘/cluster/mpi/openmpi/4.1.5-gcc/lib/mpi.mod’ opened at (1), because it
> was created by a different version of GNU Fortran
> compilation terminated.
> make[2]: ***
> [AmberTools/src/quick/src/CMakeFiles/libquick_mpi.dir/build.make:75:
> AmberTools/src/quick/src/CMakeFiles/libquick_mpi.dir/modules/quick_mpi_module.f90.o]
> Error 1
> make[1]: *** [CMakeFiles/Makefile2:8956:
> AmberTools/src/quick/src/CMakeFiles/libquick_mpi.dir/all] Error 2
> make: *** [Makefile:156: all] Error 2
>
> My modified run_cmake is:
>
> cmake $AMBER_PREFIX/amber24_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
> -DCOMPILER=GNU \
> -DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE \
> -DTRUST_SYSTEM_LIBS=TRUE \
> 2>&1 | tee cmake.log
>
> I saw the same problem in the thread
> https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Farchive.ambermd.org%2F202409%2F0142.html&data=05%7C02%7Ckeramati.m%40northeastern.edu%7Ce3a70dcaf90f475c004a08dcf8040faa%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638657943565602804%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=fLXIbU0e7Uw7Gnl5OINVOoy8t8Zg1D4l0qQAsyLLLf0%3D&reserved=0<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Farchive.ambermd.org%2F202409%2F0142.html&data=05%7C02%7Ckeramati.m%40northeastern.edu%7Ce3a70dcaf90f475c004a08dcf8040faa%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638657943565619454%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=nPrOq761kvSft6H%2B6OJKNQwDoUaghlHJTjZoVNo8knc%3D&reserved=0><http://archive.ambermd.org/202409/0142.html>
> and did what is suggested in the AmberTools/src/nlopt/CMakeLists.txt,
> but it did not work.
>
> I also tried to use a different MPI Fortran compiler (mpiifort instead
> of gfortran) with the MPI_Fortran_COMPILER flag with no success, as:
>
> -DMPI_Fortran_COMPILER=/cluster/mpi/openmpi/4.1.5-gcc/bin/mpifort
>
> Any help will be greatly appreciated.
>
> Best,
>
> Yasser
>
> Wichtiger Hinweis: Die Information in dieser E-Mail ist vertraulich.
> Sie ist ausschließlich für den Adressaten bestimmt. Sollten Sie nicht
> der für diese E-Mail bestimmte Adressat sein, unterrichten Sie bitte
> den Absender und vernichten Sie diese Mail. Vielen Dank.
> Unbeschadet der Korrespondenz per E-Mail, sind unsere Erklärungen
> ausschließlich final rechtsverbindlich, wenn sie in herkömmlicher
> Schriftform (mit eigenhändiger Unterschrift) oder durch Übermittlung
> eines solchen Schriftstücks per Telefax erfolgen.
>
> Important note: The information included in this e-mail is
> confidential. It is solely intended for the recipient. If you are not
> the intended recipient of this e-mail please contact the sender and
> delete this message. Thank you. Without prejudice of e-mail
> correspondence, our statements are only legally binding when they are
> made in the conventional written form (with personal signature) or
> when such documents are sent by fax.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7Ckeramati.m%40northeastern.edu%7Ce3a70dcaf90f475c004a08dcf8040faa%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638657943565628922%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=SyDnm%2Byb2XtMaqZfi0pkBGL07dVD30ivwGUZLP7DfFc%3D&reserved=0<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7Ckeramati.m%40northeastern.edu%7Ce3a70dcaf90f475c004a08dcf8040faa%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638657943565638644%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=7H5ukKtDOpNQZm4vo0PrHqwKBnv7rzB8V4OgNn5R3Ek%3D&reserved=0><http://lists.ambermd.org/mailman/listinfo/amber>
>
>
> --
> Yasser Almeida-Hernández, PhD
> Computational Bioengineering
> Fakultät Bio- und Chemieingenieurwesen
> Technische Universität Dortmund
> Otto-Hahn-Str. 6. Raum C1-02-R408
> 44227 Dortmund
> Phone: +49 0231 7556856
> Email: yasser.almeida.tu-dortmund.de<mailto:yasser.almeida.tu-dortmund.de>
>
> Wichtiger Hinweis: Die Information in dieser E-Mail ist vertraulich.
> Sie ist ausschließlich für den Adressaten bestimmt. Sollten Sie nicht
> der für diese E-Mail bestimmte Adressat sein, unterrichten Sie bitte
> den Absender und vernichten Sie diese Mail. Vielen Dank.
> Unbeschadet der Korrespondenz per E-Mail, sind unsere Erklärungen
> ausschließlich final rechtsverbindlich, wenn sie in herkömmlicher
> Schriftform (mit eigenhändiger Unterschrift) oder durch Übermittlung
> eines solchen Schriftstücks per Telefax erfolgen.
>
> Important note: The information included in this e-mail is
> confidential. It is solely intended for the recipient. If you are not
> the intended recipient of this e-mail please contact the sender and
> delete this message. Thank you. Without prejudice of e-mail
> correspondence, our statements are only legally binding when they are
> made in the conventional written form (with personal signature) or
> when such documents are sent by fax.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7Ckeramati.m%40northeastern.edu%7Ce3a70dcaf90f475c004a08dcf8040faa%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638657943565647877%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=ZcL4xF%2BTmi4S7Fzejijt9rt5jDD1prFcxpSywqHz1uY%3D&reserved=0<http://lists.ambermd.org/mailman/listinfo/amber>
--
Yasser Almeida-Hernández, PhD
Computational Bioengineering
Fakultät Bio- und Chemieingenieurwesen
Technische Universität Dortmund
Otto-Hahn-Str. 6. Raum C1-02-R408
44227 Dortmund
Phone: +49 0231 7556856
Email: yasser.almeida.tu-dortmund.de
Wichtiger Hinweis: Die Information in dieser E-Mail ist vertraulich. Sie ist ausschließlich für den Adressaten bestimmt. Sollten Sie nicht der für diese E-Mail bestimmte Adressat sein, unterrichten Sie bitte den Absender und vernichten Sie diese Mail. Vielen Dank.
Unbeschadet der Korrespondenz per E-Mail, sind unsere Erklärungen ausschließlich final rechtsverbindlich, wenn sie in herkömmlicher Schriftform (mit eigenhändiger Unterschrift) oder durch Übermittlung eines solchen Schriftstücks per Telefax erfolgen.
Important note: The information included in this e-mail is confidential. It is solely intended for the recipient. If you are not the intended recipient of this e-mail please contact the sender and delete this message. Thank you. Without prejudice of e-mail correspondence, our statements are only legally binding when they are made in the conventional written form (with personal signature) or when such documents are sent by fax.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7Ckeramati.m%40northeastern.edu%7Ce3a70dcaf90f475c004a08dcf8040faa%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638657943565657115%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=RE1DLcQSL6SOQ%2FeQzhMrF8aw2XFuOO20V3ZbXAPNoVs%3D&reserved=0<http://lists.ambermd.org/mailman/listinfo/amber>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 29 2024 - 11:00:03 PDT
