[Mesa-users] installing mesa as a module on a cluster
Rob Kudyba
rk3199 at columbia.edu
Fri Jul 14 14:46:22 UTC 2023
Now this:
build.log
*** Copy and paste the following information into your email to mesa-users
***
MESA Version
cat: /path/to/mesa/23.05.01/data/version_number: No such file or directory
uname -a
Linux server 4.18.0-193.el8.x86_64 #1 SMP Fri Mar 27 14:35:58 UTC 2020
x86_64 x86_64 x86_64 GNU/Linux
gfortran -v
Using built-in specs.
COLLECT_GCC=/path/to/me/mesasdk/bin/gfortran.exec
COLLECT_LTO_WRAPPER=/path/to/me/mesasdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/12.1.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /home/user/sdk2-tmp/build/gcc/configure CC= CXX=
--build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu
--target=x86_64-pc-linux-gnu --prefix=/home/user/sdk2-tmp/mesasdk
--with-gmp=/home/user/sdk2-tmp/mesasdk
--with-mpfr=/home/user/sdk2-tmp/mesasdk
--with-mpc=/home/user/sdk2-tmp/mesasdk --enable-languages=c,c++,fortran
--disable-multilib --disable-nls --disable-libsanitizer
--enable-clocale=generic
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 12.1.0 (GCC)
$MESASDK_ROOT
/path/to/me/mesasdk
MESASDK version
x86_64-linux-22.6.1
$PATH
/path/to/me/mesasdk/bin:/path/to/me/mesasdk/bin:/path/to/me/mesasdk/bin:/cm/shared/apps/slurm/current/sbin:/cm/shared/apps/slurm/current/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/path/to/me/abin:/path/to/me/bin:/path/to/me/abin
$MESA_DIR
/burg/opt/mesa/23.05.01
/path/to/me/mesa-r23.05.1/const
building const package.
make: '../tester' is up to date.
export
done
mesa/const has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/utils
building utils package.
make: '../tester' is up to date.
export
done
mesa/utils has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/math
building math package.
make: 'libmath.a' is up to date.
make: 'libmath.a' is up to date.
make: '../tester' is up to date.
export
done
mesa/math has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/mtx
building mtx package.
make: Nothing to be done for 'all'.
export
done
mesa/mtx has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/auto_diffbuilding auto_diff package.
make: '../tester' is up to date.
export
done
mesa/auto_diff has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/hdf5io
building hdf5io package.
make: Nothing to be done for 'all'.
export
done
mesa/hdf5io has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/num
building num package.
make: Nothing to be done for 'all'.
export
done
mesa/num has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/interp_1dbuilding interp_1d package.
mBreakfastake: '../tester' is up to date.
export
done
mesa/interp_1d has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/interp_2dbuilding interp_2d package.
make: Nothing to be done for 'all'.
export
done
mesa/interp_2d has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/chem
building chem package.
make: 'libchem.a' is up to date.
make: 'libchem.a' is up to date.
make: '../tester' is up to date.
export
done
mesa/chem has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/colors
building colors package.
make: 'libcolors.a' is up to date.
make: 'libcolors.a' is up to date.
make: '../tester' is up to date.
export
done
mesa/colors has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/eos
building eos package.
make: Nothing to be done for 'all'.
export
done
/path/to/me/mesa-r23.05.1/eos/eosDT_builder
make: '../ceos' is up to date.
mesa/eos has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/kap
building kap package.
make: Nothing to be done for 'all'.
export
done
make: '../ckap' is up to date.
mesa/kap has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/rates
building rates package.
make: Nothing to be done for 'all'.
export
done
mesa/rates has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/neu
building neu package.
make: 'libneu.a' is up to date.
make: 'libneu.a' is up to date.
make: Nothing to be done for 'all'.
export
done
mesa/neu has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/net
building net package.
make: Nothing to be done for 'all'.
export
done
mesa/net has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/star_databuilding star_data package.
make: '../tester' is up to date.
export
done
mesa/star_data has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/turb
building turb package.
make: '../tester' is up to date.
export
done
mesa/turb has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/atm
building atm package.
make: Nothing to be done for 'all'.
export
done
make: Nothing to be done for 'all'.
mesa/atm has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/sample
building sample package.
make: Nothing to be done for 'all'.
done
mesa/sample has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/gyre
building gyre package.
make: 'libgyre.a' is up to date.
make: 'libgyre.a' is up to date.
make: '../tester' is up to date.
export
done
mesa/gyre has been built, tested, and exported.
************************************************
/path/to/me/mesa-r23.05.1/adipls
building adipls package.
makefile:6: /burg/opt/mesa/23.05.01/utils/makefile_header: No such file or
directory
make: *** No rule to make target
'/burg/opt/mesa/23.05.01/utils/makefile_header'. Stop.
/path/to/me/mesa-r23.05.1/adipls/make
FAILED
/path/to/me/mesa-r23.05.1/adipls
./build_and_test FAILED
On Fri, Jul 14, 2023, 10:11 AM RICHARD H D TOWNSEND <townsend at astro.wisc.edu>
wrote:
> Looking through the build log, I see the system compiler is being used.
> This indicates that the SDK is not properly initialized.
>
> > On Jul 14, 2023, at 7:17 AM, Rob Kudyba via Mesa-users <
> mesa-users at lists.mesastar.org> wrote:
> >
> > <<<I'm not sure how many MESA users have any experience with
> *installing* MESA as a module but we can try our best to help!<<<
> >
> > Thanks, I saw a few folks attempt it in the archives, e.g.,
> https://lists.mesastar.org/pipermail/mesa-users/2023-May/014517.html,
> where getting it to work with an older source package.
> >
> > <<First, what is required to install MESA as a module? Do you want to
> do it with the SDK, so that loading the module also sets those environment
> variables? Or do you want to do it without the SDK and have modules load
> the dependencies?<<<<
> >
> > Ideally the latter but open to the former.
> >
> > <<<Can you explain precisely what you've done to try to build MESA, and
> attach the full `build.log` file that the `./install` scripts creates?<<<
> >
> > Just ran ./instal, with the SDK downloaded and 2 variables set:
> > cat build.log
> > *** Copy and paste the following information into your email to
> mesa-users ***
> >
> > MESA Version
> > cat: /data/version_number: No such file or directory
> >
> > uname -a
> > Linux ourserver 4.18.0-193.el8.x86_64 #1 SMP Fri Mar 27 14:35:58 UTC
> 2020 x86_64 x86_64 x86_64 GNU/Linux
> >
> > gfortran -v
> > Using built-in specs.
> > COLLECT_GCC=gfortran
> > COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper
> > OFFLOAD_TARGET_NAMES=nvptx-none
> > OFFLOAD_TARGET_DEFAULT=1
> > Target: x86_64-redhat-linux
> > Configured with: ../configure --enable-bootstrap
> --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man
> --infodir=/usr/share/info --with-bugurl=
> http://bugzilla.redhat.com/bugzilla --enable-shared
> --enable-threads=posix --enable-checking=release --enable-multilib
> --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions
> --enable-gnu-unique-object --enable-linker-build-id
> --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin
> --enable-initfini-array --with-isl --disable-libmpx
> --enable-offload-targets=nvptx-none --without-cuda-driver
> --enable-gnu-indirect-function --enable-cet --with-tune=generic
> --with-arch_32=x86-64 --build=x86_64-redhat-linux
> > Thread model: posix
> > gcc version 8.3.1 20191121 (Red Hat 8.3.1-5) (GCC)
> > $MESASDK_ROOT
> >
> >
> > MESASDK version
> > MESASDK not setup
> >
> > $PATH
> > /sbin:/bin:/usr/sbin:/usr/bin
> >
> > $MESA_DIR
> >
> >
> >
> > ****************************************************************
> > * *
> > * MESA should not be installed with root privaleges *
> > * Using sudo is a bad idea and unlikely to fix the *
> > * problem you think you have. *
> > * *
> > * If you have permission issues, *
> > * contact the mesa-users mailing list *
> > * *
> > * If you wish to install mesa in a root location *
> > * then we assume you can edit the *
> > * ./install file to remove this check *
> > * *
> > ****************************************************************
> >
> >
> > Note the typo in 'privaleges'...
> >
> >
> > On Fri, Jul 14, 2023 at 3:34 AM Warrick Ball <W.H.Ball at bham.ac.uk>
> wrote:
> > Hi Rob,
> >
> > For context, I presume what you mean is that you want to install MESA as
> an Environment Module [1], which is what many HPC systems use to allow
> users to load different versions of installed software with commands like
> >
> > $ module load MESA/r23.05.1
> >
> > I'm not sure how many MESA users have any experience with *installing*
> MESA as a module but we can try our best to help!
> >
> > First, what is required to install MESA as a module? Do you want to do
> it with the SDK, so that loading the module also sets those environment
> variables? Or do you want to do it without the SDK and have modules load
> the dependencies?
> >
> > Second, it's not clear what error you've actually encountered. The
> segment of the build log you show implies GYRE built fine but the ADIPLS
> failed to find the makefile, which seems odd. (Why would ADIPLS try to
> "build" the makefile header?) It also isn't clear that this has anything
> to do with `sudo`. Can you explain precisely what you've done to try to
> build MESA, and attach the full `build.log` file that the `./install`
> scripts creates?
> >
> > Cheers,
> > Warrick
> >
> > [1] https://modules.readthedocs.io/
> >
> > ___________
> >
> > Warrick Ball
> > Senior Research Software Engineer
> > University of Birmingham
> > W.H.Ball at bham.ac.uk
> >
> > On Fri, 14 Jul 2023, Rob Kudyba via Mesa-users wrote:
> >
> > > CAUTION: This email originated from outside the organisation. Do not
> click links or open attachments unless you recognise the sender and know
> the content is safe.
> > > I'd like to install Mesa as a module,.so users can load ad hoc, so
> multiple users could have access to it at will.
> > >
> > > On Thu, Jul 13, 2023, 9:20 PM Francis Timmes <fxt44 at mac.com> wrote:
> > > hi rob,
> > >
> > > i do not understand the relationship between root and making
> "this" (presumably all of mesa) a module. can you explain in more detail
> what you are trying to accomplish?
> > >
> > > fxt
> > >
> > >
> > >
> > >
> > > > On Jul 13, 2023, at 1:35 PM, Rob Kudyba via Mesa-users <
> mesa-users at lists.mesastar.org> wrote:
> > > >
> > > > I see the warnings to not use root.But I want to make this a
> module.
> > > >
> > > > FC ../tester
> > > > export
> > > > done
> > > >
> > > > mesa/gyre has been built, tested, and exported.
> > > >
> > > > ************************************************
> > > >
> > > > /path/to/me/mesa-r23.05.1/adipls
> > > > building adipls package.
> > > >
> > > > makefile:6: /path/to/mesa/23.05.01/utils/makefile_header: No
> such file or directory
> > > > make: *** No rule to make target
> '/path/to/mesa/23.05.01/utils/makefile_header'. Stop.
> > > >
> > > > /path/to/me/mesa-r23.05.1/adipls/make
> > > > FAILED
> > > >
> > > >
> > > > /path/to/me/mesa-r23.05.1/adipls
> > > > ./build_and_test FAILED
> > > >
> > > > Do I just remove the root check in the install script?
> > > > _______________________________________________
> > > > mesa-users at lists.mesastar.org
> > > > https://lists.mesastar.org/mailman/listinfo/mesa-users
> > > >
> > >
> > >
> > >
> > _______________________________________________
> > mesa-users at lists.mesastar.org
> > https://lists.mesastar.org/mailman/listinfo/mesa-users
> >
>
>
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