[Mesa-users] FW: Installation problem: rates build_and_test failed

Tue Mar 13 09:55:20 EDT 2018

It looks like there is a local installation of HDF5, possibly compiled from
source, that is setting the LD_LIBRARY_PATH variable. Did you install this
from the repository or by hand? Do you use hdf5 for anything but mesa? If
not you can possibly remove it because mesa provides this in the SDK.

On Mon, Mar 12, 2018 at 4:41 PM, RICHARD H D TOWNSEND via Mesa-users <
mesa-users at lists.mesastar.org> wrote:

> OK, the LD_LIBRARY_PATH variable is causing the problems. Try unsetting it:
>
> unset LD_LIBRARY_PATH
>
> ...and then run ./clean and ./install in $MESA_DIR.
>
> Longer term, you might want to find out why LD_LIBRARY_PATH is getting
> set; it's generally not a good idea to use this variable, as it can lead to
> strange behavior of the sort you're encountering.
>
> cheers,
>
> Rich
>
> > On Mar 12, 2018, at 8:22 AM, Liza Sazonova <esazono1 at jhu.edu> wrote:
> >
> >
> > Here is the output of the last two commands!
> >
> > saifa at Liza-Ubuntu:~/Documents/mesa-r10108$ ldd
> $MESA_DIR/rates/test/test_quietly
> >     linux-vdso.so.1 =>  (0x00007ffe7ab45000)
> >     liblapack.so => /home/saifa/mesasdk/lib/liblapack.so
> (0x00007fe5c68b4000)
> >     libxblas.so => /home/saifa/mesasdk/lib/libxblas.so
> (0x00007fe5c621d000)
> >     libblas.so => /home/saifa/mesasdk/lib/libblas.so
> (0x00007fe5c5f8e000)
> >     libhdf5_fortran.so.10 => /home/saifa/mesasdk/lib/libhdf5_fortran.so.10
> (0x00007fe5c5d41000)
> >     libhdf5.so.10 => /usr/local/hdf5/lib/libhdf5.so.10
> (0x00007fe5c5848000)
> >     libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fe5c562b000)
> >     libgfortran.so.4 => /home/saifa/mesasdk/lib64/libgfortran.so.4
> (0x00007fe5c52df000)
> >     libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fe5c4f89000)
> >     libgomp.so.1 => /home/saifa/mesasdk/lib64/libgomp.so.1
> (0x00007fe5c4d59000)
> >     libgcc_s.so.1 => /home/saifa/mesasdk/lib64/libgcc_s.so.1
> (0x00007fe5c4b42000)
> >     libquadmath.so.0 => /home/saifa/mesasdk/lib64/libquadmath.so.0
> (0x00007fe5c4902000)
> >     libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x00007fe5c46e3000)
> >     libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fe5c4303000)
> >     librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fe5c40fb000)
> >     libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fe5c3ef7000)
> >     /lib64/ld-linux-x86-64.so.2 (0x00007fe5c7223000)
> >
> > saifa at Liza-Ubuntu:~/Documents/mesa-r10108$ echo $LD_LIBRARY_PATH
> > /usr/local/hdf5/lib
> >
> >
> >
> > >Just a question, what was the problem and how did you fix it?
> >
> > I got this error during the installation: "configure: error: C compiler
> cannot create executables See `config.log' for more details."
> > There was a section in FAQ on the error, I fixed it with
> >
> > GCC_VERSION=`gcc --version | grep ^gcc | sed 's/^.* //g'`
> $MESASDK_ROOT/libexec/gcc/x86_64-pc-linux-gnu/$GCC_VERSION/install-tools/mkheaders
> $MESASDK_ROOT
> >
> >
> >
> > From: RICHARD H D TOWNSEND <townsend at astro.wisc.edu>
> > Sent: Monday, March 12, 2018 8:30:09 AM
> > To: Liza Sazonova
> > Cc: mesa-users at lists.mesastar.org
> > Subject: Re: [Mesa-users] FW: Installation problem: rates build_and_test
> failed
> >
> > Hi Liza --
> >
> > One other thing to try: can you post the output of the following two
> commands:
> >
> > ldd $MESA_DIR/rates/test/test_quietly
> >
> > echo $LD_LIBRARY_PATH
> >
> > cheers,
> >
> > Rich
> >
> > > On Mar 12, 2018, at 7:07 AM, Liza Sazonova via Mesa-users <
> mesa-users at lists.mesastar.org> wrote:
> > >
> > > Hello everyone,
> > >
> > > I am still trying to fix the problem – and I just realized that
> somehow I started replying directly to Richard rather than to the entire
> mailing list (is there a way to make sure it doesn’t just reply one person?)
> > > Anyway, any help would be appreciated!
> > >
> > > Thank you,
> > > Liza
> > >
> > > From: Liza Sazonova
> > > Sent: Friday, March 9, 2018 6:49:46 PM
> > > To: RICHARD H D TOWNSEND
> > > Subject: Re: [Mesa-users] Installation problem: rates build_and_test
> failed
> > >
> > > Hi Rich,
> > >
> > > That didn't seem to fix it, I'm getting the same error unfortunately.
> > >
> > > Cheers,
> > > Liza
> > > From: RICHARD H D TOWNSEND <townsend at astro.wisc.edu>
> > > Sent: Friday, March 9, 2018 6:41:23 PM
> > > To: Liza Sazonova
> > > Subject: Re: [Mesa-users] Installation problem: rates build_and_test
> failed
> > >
> > >
> > > Hi Liza --
> > >
> > > Thanks for the info. Everything looks good here, so I was probably
> wrong!
> > >
> > > An alternative suggestion: try running './clean' in the $MESA_DIR
> directory, prior to running './install'.
> > >
> > > cheers,
> > >
> > > Rich
> > >
> > > > On Mar 9, 2018, at 5:36 PM, Liza Sazonova <esazono1 at jhu.edu> wrote:
> > > >
> > > > Here are all of them:
> > > >
> > > > saifa at Liza-Ubuntu:~/Documents/mesa-r10108$ which gcc
> > > > /home/saifa/mesasdk/bin/gcc
> > > >
> > > > saifa at Liza-Ubuntu:~/Documents/mesa-r10108$ gcc -v
> > > > Using built-in specs.
> > > > COLLECT_GCC=/home/saifa/mesasdk/bin/gcc.exec
> > > > COLLECT_LTO_WRAPPER=/home/saifa/mesasdk/bin/../libexec/
> gcc/x86_64-pc-linux-gnu/7.2.0/lto-wrapper
> > > > Target: x86_64-pc-linux-gnu
> > > > Configured with: /root/mesasdk-src/gcc/configure CC=gcc
> --build=x86_64-pc-linux-gnu --prefix=/root/mesasdk --with-gmp=/root/mesasdk
> --with-mpfr=/root/mesasdk --with-mpc=/root/mesasdk --enable-languages=c,c++,fortran
> --disable-multilib --disable-nls --disable-libsanitizer
> --enable-clocale=generic
> > > > Thread model: posix
> > > > gcc version 7.2.0 (GCC)
> > > >
> > > > saifa at Liza-Ubuntu:~/Documents/mesa-r10108$ which gfortran
> > > > /home/saifa/mesasdk/bin/gfortran
> > > >
> > > > saifa at Liza-Ubuntu:~/Documents/mesa-r10108$ gfortran -v
> > > > Using built-in specs.
> > > > COLLECT_GCC=/home/saifa/mesasdk/bin/gfortran.exec
> > > > COLLECT_LTO_WRAPPER=/home/saifa/mesasdk/bin/../libexec/
> gcc/x86_64-pc-linux-gnu/7.2.0/lto-wrapper
> > > > Target: x86_64-pc-linux-gnu
> > > > Configured with: /root/mesasdk-src/gcc/configure CC=gcc
> --build=x86_64-pc-linux-gnu --prefix=/root/mesasdk --with-gmp=/root/mesasdk
> --with-mpfr=/root/mesasdk --with-mpc=/root/mesasdk --enable-languages=c,c++,fortran
> --disable-multilib --disable-nls --disable-libsanitizer
> --enable-clocale=generic
> > > > Thread model: posix
> > > > gcc version 7.2.0 (GCC)
> > > >
> > > > saifa at Liza-Ubuntu:~/Documents/mesa-r10108$ mesasdk_hdf5_link
> > > > -L/home/saifa/mesasdk/lib -lhdf5_fortran -lhdf5 -lz
> > > >
> > > > Thanks!
> > > > Liza
> > > >
> > > >
> > > > From: RICHARD H D TOWNSEND <townsend at astro.wisc.edu>
> > > > Sent: Friday, March 9, 2018 6:31:26 PM
> > > > To: Liza Sazonova
> > > > Cc: Liza Sazonova via Mesa-users
> > > > Subject: Re: [Mesa-users] Installation problem: rates build_and_test
> failed
> > > >
> > > >
> > > > Hi Liza --
> > > >
> > > > Can you run the following commands, and post the output:
> > > >
> > > > which gcc
> > > > gcc -v
> > > >
> > > > which gfortran
> > > > gfortran -v
> > > >
> > > > mesasdk_hdf5_link
> > > >
> > > > cheers,
> > > >
> > > > Rich
> > > >
> > > > > On Mar 9, 2018, at 5:26 PM, Liza Sazonova <esazono1 at jhu.edu>
> wrote:
> > > > >
> > > > > Hi Rich,
> > > > >
> > > > > Thanks for the fast response!
> > > > > I've followed all steps in http://www.astro.wisc.edu/~
> townsend/static.php?ref=mesasdk
> > mad star - MESA SDK
> > www.astro.wisc.edu
> > MESA SDK. The MESA SDK is a collection of compilers and run-time
> libraries which make it easy to install and use the MESA stellar evolution
> code.
> >
> > > > > so it should be installed properly, I don't immediately see
> anything wrong with it at least. Is there something I can check to see what
> can the problem with my sdk be?
> > > > >
> > > > >
> > > > > From: RICHARD H D TOWNSEND <townsend at astro.wisc.edu>
> > > > > Sent: Friday, March 9, 2018 6:15:19 PM
> > > > > To: Liza Sazonova; Liza Sazonova via Mesa-users
> > > > > Subject: Re: [Mesa-users] Installation problem: rates
> build_and_test failed
> > > > >
> > > > >
> > > > > Hi Liza --
> > > > >
> > > > > I'm guessing the MESA SDK isn't properly installed.
> > > > >
> > > > > cheers,
> > > > >
> > > > > Rich
> > > > >
> > > > > > On Mar 9, 2018, at 4:57 PM, Liza Sazonova via Mesa-users <
> mesa-users at lists.mesastar.org> wrote:
> > > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > I am trying to reinstall MESA after updating Ubuntu and I keep
> getting installation issues.
> > > > > > I've fixed the error with my C compiled, but now I get this:
> > > > > >
> > > > > >  -lmtx -lconst -lutils `mesasdk_lapack_link` `mesasdk_blas_link`
> `mesasdk_hdf5_link`
> > > > > > ../utils/build_and_test_parallel: line 56:  7588 Aborted
>          (core dumped) ./test_quietly &> test_quietly.txt
> > > > > > /home/saifa/Documents/mesa-r10108/rates/test
> > > > > > FAILED
> > > > > > /home/saifa/Documents/mesa-r10108/rates
> > > > > > ./build_and_test FAILED
> > > > > >
> > > > > > There is no tmp.txt file in my rates/test folder. I attached the
> output from ./tester 2>&1 | tee tester.log
> > > > > > Thank you in advance!
> > > > > >
> > > > > > Best regards,
> > > > > > Liza Sazonova
> > > > > >
> > > > > >
> > > > > >
> > > > > > <tester.log>_______________________________________________
> > > > > > mesa-users at lists.mesastar.org
> > > > > > https://lists.mesastar.org/mailman/listinfo/mesa-users
> > Mesa-users Info Page - lists.mesastar.org
> > lists.mesastar.org
> > Mesa-users -- List for users of the MESA stellar evolution code About
> Mesa-users
> >
> > >
> > >
> > > _______________________________________________
> > > mesa-users at lists.mesastar.org
> > > https://lists.mesastar.org/mailman/listinfo/mesa-users
> > Mesa-users Info Page - lists.mesastar.org
> > lists.mesastar.org
> > Mesa-users -- List for users of the MESA stellar evolution code About
> Mesa-users
> >
> >
>
> _______________________________________________
> mesa-users at lists.mesastar.org
> https://lists.mesastar.org/mailman/listinfo/mesa-users
>
>

-- 
Amber Lauer
Postdoctoral Researcher
Triangle University Nuclear Lab
Duke University
amber.lauer at tunl.duke.edu <amber.lauer at duke.edu>
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