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%7Ce00479297495467bc44f08dcf1ddb105%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638651181777772120%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kX6JB0mxJ%2F9nNnVs%2BppX5iUeNQpi5FesmzcSx4vN49s%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
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--
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.
_______________________________________________
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Received on Tue Oct 29 2024 - 03:30:01 PDT
