[mesa-users] mesa install mesa/star fail
Richard Townsend
townsend at astro.wisc.edu
Thu Aug 6 21:47:34 EDT 2015
Hi Amber —
Martyn and I ended up resolving this off-line — turns out the culprit was running the install script via ‘sudo’. The root account didn’t have the SDK initialization commands in its login scripts, and so the SDK compiler/link commands/libraries weren’t being found.
cheers,
Rich
> On Aug 7, 2015, at 2:42 AM, Amber Lauer <alauer1 at tigers.lsu.edu> wrote:
>
> Isn't the zlib-dev also required? I seem to recall that it is.
>
> On Thu, Jul 30, 2015 at 8:01 AM, Martyn Brake <mdb at astro.ex.ac.uk <mailto:mdb at astro.ex.ac.uk>> wrote:
> Hi Richard,
>
> Thank you for replying. The links work from the terminal, so which gfortrans gives:
> /opt/mesasdk/bin/gfortran
>
> They just don't seem to be recognised from the makefile.
>
> Cheers,
> Martyn
>
> On 30 Jul 2015, at 11:44, Richard Townsend <townsend at astro.wisc.edu <mailto:townsend at astro.wisc.edu>> wrote:
>
>> If the _link commands weren’t being recognized, then it’s likely that the SDK isn’t installed properly.
>>
>> What output do you get from `which gfortran`?
>>
>>> On Jul 30, 2015, at 10:04 AM, Martyn Brake <mdb at astro.ex.ac.uk <mailto:mdb at astro.ex.ac.uk>> wrote:
>>>
>>> Ok,
>>>
>>> Tried from the beginning, all prereq definitely installed.
>>>
>>> Had to replace `mesasdk_lapack_link`, mesasdk_blas_link`, `mesasdk_pgplot_link` and `mesasdk_se_link` as they were not being recognised in the make file
>>>
>>> # step 3) specify which BLAS and LAPACK libraries to use for mesa/mtx
>>>
>>> WHICH_LAPACK =
>>> WHICH_BLAS =
>>> LOAD_LAPACK = /opt/mesasdk/lib/liblapack.a /opt/mesasdk/lib/libxblas.a /opt/mesasdk/lib/libblas.a
>>> LOAD_BLAS = /opt/mesasdk/lib/libblas.a
>>>
>>>
>>> # step 4) do you want to use PGPLOT with mesa/star? $
>>>
>>> USE_PGSTAR = YES
>>> LOAD_PGPLOT = -L/opt/mesasdk/lib -lpgplot -lX11
>>>
>>>
>>> # step 5) do you want to use SE with mesa/star? (ask Falk about it)
>>>
>>> USE_SE = NO
>>> #USE_SE = YES
>>> LOAD_SE = -L/opt/mesasdk/lib -lse -L/opt/mesasdk/lib -lhdf5_fortran -lhdf5 -lz
>>> INCLUDE_SE = -I${MESASDK_ROOT}/include
>>>
>>> Still get the following:
>>> gfortran -fno-range-check -fmax-errors=100 -fprotect-parens -fno-sign-zero -fopenmp -o ../star \
>>> run_star_extras.o run_star.o run.o -L../../make -lstar -L../../../lib -lionization -latm -lcolors -lmlt -lnse -lnet -leos -lkap -lrates -lneu -lchem -linterp_2d -linterp_1d -lnum -lf2crlibm -lcrlibm -lmtx -lconst -lutils -lmesaklu /opt/mesasdk/lib/liblapack.a /opt/mesasdk/lib/libxblas.a /opt/mesasdk/lib/libblas.a /opt/mesasdk/lib/libblas.a -L/opt/mesasdk/lib -lpgplot -lX11 -L/opt/mesasdk/lib -lse -L/opt/mesasdk/lib -lhdf5_fortran -lhdf5 -lz
>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `deflateInit2_'
>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `deflate'
>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `deflateEnd'
>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `crc32'
>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `inflate'
>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `inflateInit_'
>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `inflateEnd'
>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `inflateReset'
>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `deflateReset'
>>> collect2: error: ld returned 1 exit status
>>> make: *** [star] Error 1
>>>
>>> FAILED
>>>
>>>
>>> /opt/mesa/star/test
>>> FAILED
>>>
>>>
>>> Any help would be appreciated.
>>>
>>> Kind regards,
>>> Martyn
>>>
>>> On 29 Jul 2015, at 16:56, Martyn Brake <mdb at astro.ex.ac.uk <mailto:mdb at astro.ex.ac.uk>> wrote:
>>>
>>>> Hi Josiah,
>>>>
>>>> Many thanks for your help. Double checked the prerequisites reinstalled zlib using following
>>>>
>>>> sudo apt-get install --reinstall zlibc zlib1g zlib1g-dev
>>>>
>>>> did a ./clean followed by ./install
>>>>
>>>> Still errors at same point. Will double check everything tomorrow.
>>>>
>>>> Cheers,
>>>> Martyn
>>>> On 29 Jul 2015, at 16:32, Josiah W. Schwab <jwschwab at berkeley.edu <mailto:jwschwab at berkeley.edu>> wrote:
>>>>
>>>>> Looks like you didn't install the prerequisites, notably at least zlib.
>>>>>
>>>>> http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk#Pre-requisites\ <http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk#Pre-requisites%5C>
>>>>>
>>>>> Josiah
>>>>>
>>>>> On Wed, Jul 29, 2015 at 8:05 AM, Martyn Brake <mdb at astro.ex.ac.uk <mailto:mdb at astro.ex.ac.uk>> wrote:
>>>>> Hello,
>>>>>
>>>>> I am trying to get mesa installed. I have the latest versions of mesasdk installed and checked out the latest build from svn.
>>>>>
>>>>> I get the following error:
>>>>> gfortran -fno-range-check -fmax-errors=100 -fprotect-parens -fno-sign-zero -fopenmp -o ../star \
>>>>> run_star_extras.o run_star.o run.o -L../../make -lstar -L../../../lib -lionization -latm -lcolors -lmlt -lnse -lnet -leos -lkap -lrates -lneu -lchem -linterp_2d -linterp_1d -lnum -lf2crlibm -lcrlibm -lmtx -lconst -lutils -lmesaklu /opt/mesasdk/lib/liblapack.a /opt/mesasdk/lib/libxblas.a /opt/mesasdk/lib/libblas.a /opt/mesasdk/lib/libblas.a -L/opt/mesasdk/lib -lpgplot -lX11 -L/opt/mesasdk/lib -lse -L/opt/mesasdk/lib -lhdf5_fortran -lhdf5 -lz
>>>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `deflateInit2_'
>>>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `deflate'
>>>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `deflateEnd'
>>>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `crc32'
>>>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `inflate'
>>>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `inflateInit_'
>>>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `inflateEnd'
>>>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `inflateReset'
>>>>> /opt/mesasdk/lib/libpgplot.so: undefined reference to `deflateReset'
>>>>> collect2: error: ld returned 1 exit status
>>>>> make: *** [star] Error 1
>>>>>
>>>>> FAILED
>>>>>
>>>>>
>>>>> /opt/mesa/star/test
>>>>> FAILED
>>>>>
>>>>>
>>>>> /opt/mesa/star
>>>>> ./build_and_test FAILED
>>>>>
>>>>> Could somebody let me know where/why this is failing?
>>>>>
>>>>> Thanks,
>>>>> Martyn
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> _______________________________________________
>>>>> mesa-users mailing list
>>>>> mesa-users at lists.sourceforge.net <mailto:mesa-users at lists.sourceforge.net>
>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users <https://lists.sourceforge.net/lists/listinfo/mesa-users>
>>>>>
>>>>
>>>> Martyn Brake
>>>>
>>>> Department of Astrophysics
>>>> University of Exeter
>>>>
>>>> Email: mdb at astro.ex.ac.uk <mailto:mdb at astro.ex.ac.uk>
>>>> Telephone: 01392 725511
>>>>
>>>> ------------------------------------------------------------------------------
>>>> _______________________________________________
>>>> mesa-users mailing list
>>>> mesa-users at lists.sourceforge.net <mailto:mesa-users at lists.sourceforge.net>
>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users <https://lists.sourceforge.net/lists/listinfo/mesa-users>
>>>
>>> Martyn Brake
>>>
>>> Department of Astrophysics
>>> University of Exeter
>>>
>>> Email: mdb at astro.ex.ac.uk <mailto:mdb at astro.ex.ac.uk>
>>> Telephone: 01392 725511
>>>
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> mesa-users mailing list
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>>> https://lists.sourceforge.net/lists/listinfo/mesa-users <https://lists.sourceforge.net/lists/listinfo/mesa-users>
>>
>
> Martyn Brake
>
> Department of Astrophysics
> University of Exeter
>
> Email: mdb at astro.ex.ac.uk <mailto:mdb at astro.ex.ac.uk>
> Telephone: 01392 725511
>
>
> ------------------------------------------------------------------------------
>
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>
>
>
>
> --
> Amber Lauer. M.S. Physics
> PhD Candidate,
> Dept. of Physics & Astronomy,
> Louisiana State University
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