I did run ./clean_build before re-running the cmake command. "DFORCE_DISABLE_LIBS=perlmol" itself seems not enough to disable permol module. I manually enforce it by set "NEED_perlmol=FALSE" in the 3rdparty cmake file and then cmake finished fine. During the "make install" I notice some other compiler/lib related issues. I can try to fix them.
Thanks your advise!
Wei Jiang, PhD, Computational Science Division
Argonne National Laboratory
9700S, Cass Ave, Lemont, IL60439
630-252-8688<callto:630-252-8688> (office)
630-252-7121<callto:630-252-7121> (fax)
________________________________
From: Masoud Keramati <keramati.m.northeastern.edu>
Sent: Thursday, December 12, 2024 4:13 PM
To: Jiang, Wei <wjiang.alcf.anl.gov>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Compiling error of Amber24 on Linux
Hmmm. . . Check cmake. log to see if perlmol is disabled. Also do not forget to use ./clean_build before re-running the cmake command. Best, Masoud From: Jiang, Wei <wjiang@ alcf. anl. gov> Sent: Thursday, December 12, 2024 16: 57 To: Masoud
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Hmmm...
Check cmake.log to see if perlmol is disabled.
Also do not forget to use ./clean_build before re-running the cmake command.
Best,
Masoud
________________________________
From: Jiang, Wei <wjiang.alcf.anl.gov>
Sent: Thursday, December 12, 2024 16:57
To: Masoud Keramati <keramati.m.northeastern.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Compiling error of Amber24 on Linux
Thanks! But I still get the same error "Determining if the Perl module Chemistry::Mol exists failed with the following error output:
Can't locate Chemistry/Mol.pm in .INC (you may need to install the Chemistry::Mol module)".
This is my modified run_cmake
cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=GNU \
-DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DFORCE_DISABLE_LIBS=perlmol -DDOWNLOAD_MINICONDA=TRUE \
2>&1 | tee cmake.log
Thanks!
Wei Jiang, PhD, Computational Science Division
Argonne National Laboratory
9700S, Cass Ave, Lemont, IL60439
630-252-8688<callto:630-252-8688> (office)
630-252-7121<callto:630-252-7121> (fax)
________________________________
From: Masoud Keramati <keramati.m.northeastern.edu>
Sent: Thursday, December 12, 2024 3:05 PM
To: Jiang, Wei <wjiang.alcf.anl.gov>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Compiling error of Amber24 on Linux
Hi, Add "-DFORCE_DISABLE_LIBS=perlmol" to your cmake command. Best, Masoud From: Jiang, Wei via AMBER <amber@ ambermd. org> Sent: Thursday, December 12, 2024 15: 10 To: amber@ ambermd. org <amber@ ambermd. org> Subject: [AMBER]
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Hi,
Add "-DFORCE_DISABLE_LIBS=perlmol" to your cmake command.
Best,
Masoud
________________________________
From: Jiang, Wei via AMBER <amber.ambermd.org>
Sent: Thursday, December 12, 2024 15:10
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Compiling error of Amber24 on Linux
Hi, I tried to build Amber24 on a large Linux cluster but was running issues with missing PerlMol (perl chemistry) module. The system software administrator confirmed that this module can not be provided as it is not available for SUSE linux as a RPM (Red Hat Package Manager). However, manually installing this module appears convoluted due to complex Perl module dependencies/permissions, and has never passed yet. Can anybody advise how to fix/avoid this issue to build Amber24?
Thanks!
Wei
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Received on Fri Dec 13 2024 - 08:00:02 PST
