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

RICHARD H D TOWNSEND townsend at astro.wisc.edu
Mon Mar 12 16:41:10 EDT 2018 

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
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> > 
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