Hi,
On Rocky Linux 8.6 HPC system we try to compile Yambo 5.2.1 version gives error about petsc. Configure and make steps are attached on file yambo_configure_make_log.txt.
compile_yambo.log and compile_petsc-3.17.4.log are attached too.
Compiling Yambo 5.2.1 petsc error
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Forum rules
If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
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aziz.ogutlu
- Posts: 7
- Joined: Mon Apr 17, 2023 3:26 pm
Compiling Yambo 5.2.1 petsc error
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Aziz Ogutlu
Linux System Administrator
Linux System Administrator
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Nicola Spallanzani
- Posts: 63
- Joined: Thu Nov 21, 2019 10:15 am
Re: Compiling Yambo 5.2.1 petsc error
Dear Aziz,
I apologize for the very late response, but I encountered difficulties in reproducing the same error.
The issue is only seemingly caused by PETSc. In reality, the problem lies upstream with the compilation of LAPACK. If you check the file "log/compile_lapack-3.9.1.log", you should see that it complains about the lack of CMake.
To successfully compile LAPACK in shared mode (for PETSc), it is necessary to have CMake available. So, try installing or loading the CMake module and start the compilation from scratch. By starting from scratch, I mean deleting the YAMBO folder and recreating it by unpacking the tarball again.
Best,
Nicola
PS: please sign your post with your name and affiliation, this is a rule of the forum. You can do once for all by filling the signature in your user profile.
I apologize for the very late response, but I encountered difficulties in reproducing the same error.
The issue is only seemingly caused by PETSc. In reality, the problem lies upstream with the compilation of LAPACK. If you check the file "log/compile_lapack-3.9.1.log", you should see that it complains about the lack of CMake.
To successfully compile LAPACK in shared mode (for PETSc), it is necessary to have CMake available. So, try installing or loading the CMake module and start the compilation from scratch. By starting from scratch, I mean deleting the YAMBO folder and recreating it by unpacking the tarball again.
Best,
Nicola
PS: please sign your post with your name and affiliation, this is a rule of the forum. You can do once for all by filling the signature in your user profile.
Nicola Spallanzani, PhD
S3 Centre, Istituto Nanoscienze CNR and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu
S3 Centre, Istituto Nanoscienze CNR and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu
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aziz.ogutlu
- Posts: 7
- Joined: Mon Apr 17, 2023 3:26 pm
Re: Compiling Yambo 5.2.1 petsc error
Dear Nicola,
We had holiday and I could not look to issue until today. I followed your instruction and recompiled from scratch but I got same error about petsc on first message.
And libxc download link is broken on lib/archive/package.list file.
I'm editing libxc like below:
#url_libxc=https://www.tddft.org/programs/libxc/do ... all_libxc)
url_libxc=https://www.cp2k.org/static/downloads/$(tarball_libxc)
Best regards,
Aziz
We had holiday and I could not look to issue until today. I followed your instruction and recompiled from scratch but I got same error about petsc on first message.
And libxc download link is broken on lib/archive/package.list file.
I'm editing libxc like below:
#url_libxc=https://www.tddft.org/programs/libxc/do ... all_libxc)
url_libxc=https://www.cp2k.org/static/downloads/$(tarball_libxc)
Best regards,
Aziz
Aziz Ogutlu
Linux System Administrator
Linux System Administrator