[mesa-users] Question

Broxton Miles bjmiles at crimson.ua.edu
Wed Jun 24 12:55:47 EDT 2015 

After you downloaded it, did you follow the steps for unpacking and
initializing the mesasdk? You need to do that before you try to install
MESA.

The instructions from the mesasdk site for the version you've downloaded:

   - Download the package from the table above
   <http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk#linux-download>
   - Extract it using the command tar xvfz *package_name* -C ~/ (note
   that's a tilde in front of the slash!)
   - Set the path to the SDK:
      - For the C shell: setenv MESASDK_ROOT ~/mesasdk
      - For the Bourne shell: export MESASDK_ROOT=~/mesasdk
   - Initialize the SDK (also checks compatibility):
      - For the C shell: source $MESASDK_ROOT/bin/mesasdk_init.csh
      - For the Bourne shell: source $MESASDK_ROOT/bin/mesasdk_init.sh
   - Check that the SDK is properly installed by running gfortran --version.
   The first line of the output should look something like this:
   GNU Fortran (GCC) 4.9.2 20141023 (prerelease)
   If it *doesn't*, then you should consult the Troubleshooting
   <http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk#Troubleshooting>
section
   below

Broxton


On Wed, Jun 24, 2015 at 12:49 PM, Liliana Novais <linovais at gmail.com> wrote:

> I just dowload it the one: mesasd-x86_64-linux-20141212.tar.gz...
>
> I did ./clean and followed the instruction on the instalation guide....
>
> http://mesastar.org/teaching-materials/graduate-course-berkeley/installation-guide#sec-2-2
>
> It started to install then block on the tests:
> test_banded.o: In function `__test_banded_MOD_test_med':
> /home/lnovais/mesa/mtx/test/make/../src/test_banded.f:134: undefined
> reference to `dgbsv_'
> test_square.o: In function `__test_square_MOD_test_square1':
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:181: undefined
> reference to `dgetrf_'
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:187: undefined
> reference to `dgetrs_'
> test_square.o: In function `__test_square_MOD_test_square2':
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:139: undefined
> reference to `dgetrf_'
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:144: undefined
> reference to `dgetrs_'
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:150: undefined
> reference to `dgetrf_'
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:155: undefined
> reference to `dgetrs_'
> test_square.o: In function `__test_square_MOD_test_square_inv':
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:68: undefined
> reference to `dgetrf_'
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:75: undefined
> reference to `dgetrs_'
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:81: undefined
> reference to `dgemv_'
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:94: undefined
> reference to `dgetrf_'
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:101: undefined
> reference to `dgetrs_'
> /home/lnovais/mesa/mtx/test/make/../src/test_square.f:106: undefined
> reference to `dgemv_'
> collect2: error: ld returned 1 exit status
> makefile:35: recipe for target 'tester' failed
> make: *** [tester] Error 1
>
> /home/lnovais/mesa/mtx/test
> FAILED
>
>
> /home/lnovais/mesa/mtx
> ./build_and_test FAILED
>
>
>
> 2015-06-24 17:45 GMT+01:00 Broxton Miles <bjmiles at crimson.ua.edu>:
>
>> This is the output of the gfortan
>>> [lnovais at new-host home]$ gfortran -v
>>> Using built-in specs.
>>> COLLECT_GCC=gfortran
>>>
>>> COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/5.1.1/lto-wrapper
>>> Target: x86_64-redhat-linux
>>> Configured with: ../configure --enable-bootstrap
>>> --enable-languages=c,c++,objc,obj-c++,fortran,ada,go,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-linker-hash-style=gnu --enable-plugin --enable-initfini-array
>>> --disable-libgcj --with-default-libstdcxx-abi=c++98 --with-isl
>>> --enable-libmpx --enable-gnu-indirect-function --with-tune=generic
>>> --with-arch_32=i686 --build=x86_64-redhat-linux
>>> Thread model: posix
>>> gcc version 5.1.1 20150612 (Red Hat 5.1.1-3) (GCC)
>>> I just restarted the instalation... and it gives me back the error....
>>
>> You're not initializing the mesasdk correctly. If you have it initialized
>> correctly the output should be something like
>>
>>> Using built-in specs.
>>>
>>> COLLECT_GCC=/ccs/home/bjmiles/mesasdk/bin/gfortran.exec
>>>
>>>
>>> COLLECT_LTO_WRAPPER=/autofs/nccs-svm1_home1/bjmiles/mesasdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/4.9.3/lto-wrapper
>>>
>>> Target: x86_64-pc-linux-gnu
>>>
>>> Configured with: ./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
>>>
>>> Thread model: posix
>>>
>>> gcc version 4.9.3 20141212 (prerelease) (GCC)
>>>
>>
>>   And like Rich said you need the latest release version of MESA.
>>
>> Broxton
>>
>> On Wed, Jun 24, 2015 at 12:37 PM, Liliana Novais <linovais at gmail.com>
>> wrote:
>>
>>> This is the output of the gfortan
>>>
>>> [lnovais at new-host home]$ gfortran -v
>>> Using built-in specs.
>>> COLLECT_GCC=gfortran
>>>
>>> COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/5.1.1/lto-wrapper
>>> Target: x86_64-redhat-linux
>>> Configured with: ../configure --enable-bootstrap
>>> --enable-languages=c,c++,objc,obj-c++,fortran,ada,go,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-linker-hash-style=gnu --enable-plugin --enable-initfini-array
>>> --disable-libgcj --with-default-libstdcxx-abi=c++98 --with-isl
>>> --enable-libmpx --enable-gnu-indirect-function --with-tune=generic
>>> --with-arch_32=i686 --build=x86_64-redhat-linux
>>> Thread model: posix
>>> gcc version 5.1.1 20150612 (Red Hat 5.1.1-3) (GCC)
>>>
>>> I just restarted the instalation... and it gives me back the error....
>>>
>>> 2015-06-24 17:33 GMT+01:00 Broxton Miles <bjmiles at crimson.ua.edu>:
>>>
>>>> Let's keep this on the mailing list so make sure you're hitting reply
>>>> all.
>>>>
>>>>  I started again and know I got the following error:
>>>>> /home/lnovais/mesasdk/trunk/utils
>>>>> building utils package.
>>>>> gfortran -fno-range-check  -fopenmp  -I../public -I../private
>>>>> -I../../include -Wunused-value -Werror -W -fimplicit-none   -fbounds-check
>>>>> -O2 -g -c -ffree-form   ../public/utils_def.f
>>>>> gfortran -fno-range-check  -fopenmp  -I../public -I../private
>>>>> -I../../include -Wunused-value -Werror -W -fimplicit-none   -fbounds-check
>>>>> -O2 -g -c -ffree-form   ../private/utils_isnan_okay.f
>>>>> ../private/utils_isnan_okay.f:43.36:
>>>>>          is_real_inf = (2*x==x .and. x /= 0)
>>>>>                                     1
>>>>> Warning: Inequality comparison for REAL(4) at (1)
>>>>> ../private/utils_isnan_okay.f:43.24:
>>>>>          is_real_inf = (2*x==x .and. x /= 0)
>>>>>                         1
>>>>> Warning: Equality comparison for REAL(4) at (1)
>>>>> ../private/utils_isnan_okay.f:37.31:
>>>>>          is_inf = (2*x==x .and. x /= 0)
>>>>>                                1
>>>>> Warning: Inequality comparison for REAL(8) at (1)
>>>>> ../private/utils_isnan_okay.f:37.19:
>>>>>          is_inf = (2*x==x .and. x /= 0)
>>>>>                    1
>>>>> Warning: Equality comparison for REAL(8) at (1)
>>>>> makefile:42: recipe for target 'utils_isnan_okay.o' failed
>>>>> make: *** [utils_isnan_okay.o] Error 1
>>>>> /home/lnovais/mesasdk/trunk/utils/make
>>>>> FAILED
>>>>>
>>>>> /home/lnovais/mesasdk/trunk/utils
>>>>> ./build_and_test FAILED
>>>>
>>>>
>>>> I'm not entirely sure of what could be causing that. What is the output
>>>> of gfortran --version and echo $MESASDK_ROOT?
>>>>
>>>> Broxton
>>>>
>>>>
>>>>
>>>> On Wed, Jun 24, 2015 at 12:22 PM, Liliana Novais <linovais at gmail.com>
>>>> wrote:
>>>>
>>>>> I started again and know I got the following error:
>>>>>
>>>>> /home/lnovais/mesasdk/trunk/utils
>>>>> building utils package.
>>>>>
>>>>> gfortran -fno-range-check  -fopenmp  -I../public -I../private
>>>>> -I../../include -Wunused-value -Werror -W -fimplicit-none   -fbounds-check
>>>>> -O2 -g -c -ffree-form   ../public/utils_def.f
>>>>> gfortran -fno-range-check  -fopenmp  -I../public -I../private
>>>>> -I../../include -Wunused-value -Werror -W -fimplicit-none   -fbounds-check
>>>>> -O2 -g -c -ffree-form   ../private/utils_isnan_okay.f
>>>>> ../private/utils_isnan_okay.f:43.36:
>>>>>
>>>>>          is_real_inf = (2*x==x .and. x /= 0)
>>>>>                                     1
>>>>> Warning: Inequality comparison for REAL(4) at (1)
>>>>> ../private/utils_isnan_okay.f:43.24:
>>>>>
>>>>>          is_real_inf = (2*x==x .and. x /= 0)
>>>>>                         1
>>>>> Warning: Equality comparison for REAL(4) at (1)
>>>>> ../private/utils_isnan_okay.f:37.31:
>>>>>
>>>>>          is_inf = (2*x==x .and. x /= 0)
>>>>>                                1
>>>>> Warning: Inequality comparison for REAL(8) at (1)
>>>>> ../private/utils_isnan_okay.f:37.19:
>>>>>
>>>>>          is_inf = (2*x==x .and. x /= 0)
>>>>>                    1
>>>>> Warning: Equality comparison for REAL(8) at (1)
>>>>> makefile:42: recipe for target 'utils_isnan_okay.o' failed
>>>>> make: *** [utils_isnan_okay.o] Error 1
>>>>>
>>>>> /home/lnovais/mesasdk/trunk/utils/make
>>>>> FAILED
>>>>>
>>>>>
>>>>> /home/lnovais/mesasdk/trunk/utils
>>>>> ./build_and_test FAILED
>>>>>
>>>>>
>>>>> 2015-06-24 16:49 GMT+01:00 Liliana Novais <linovais at gmail.com>:
>>>>>
>>>>>> I went to that site and downloaded it then I started to install
>>>>>> following the steps I'm gointo to erase all and start again because I
>>>>>> must had made a mistake somewhere
>>>>>>
>>>>>>
>>>>>> 2015-06-24 16:43 GMT+01:00 Broxton Miles <bjmiles at crimson.ua.edu>:
>>>>>>
>>>>>>> Liliana,
>>>>>>>
>>>>>>> I just have to download it? or do I need to run it also?
>>>>>>>>
>>>>>>>> I followed the steps on this site:
>>>>>>>>
>>>>>>>> http://joaofariaresearch.weebly.com/1/post/2012/04/installing-mesa.html
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Yeah, you have to download it and install it/initialize it.
>>>>>>>
>>>>>>> I would say follow the instructions on the sdk site that pertain to
>>>>>>> your particular system:
>>>>>>>
>>>>>>>
>>>>>>> http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk#toc-Downloads
>>>>>>>
>>>>>>> Try following those instructions and those of the official MESA page
>>>>>>> <http://mesa.sourceforge.net/prereqs.html> and then report back
>>>>>>> your results, and we'll go from there.
>>>>>>>
>>>>>>> Broxton
>>>>>>>
>>>>>>> On Wed, Jun 24, 2015 at 11:37 AM, Liliana Novais <linovais at gmail.com
>>>>>>> > wrote:
>>>>>>>
>>>>>>>> I just have to download it? or do I need to run it also?
>>>>>>>>
>>>>>>>> I followed the steps on this site:
>>>>>>>>
>>>>>>>> http://joaofariaresearch.weebly.com/1/post/2012/04/installing-mesa.html
>>>>>>>>
>>>>>>>> 2015-06-24 16:34 GMT+01:00 Broxton Miles <bjmiles at crimson.ua.edu>:
>>>>>>>>
>>>>>>>>> Have you downloaded and initialized the mesasdk?
>>>>>>>>>
>>>>>>>>> The reason I ask is:
>>>>>>>>>
>>>>>>>>>> make: gfortran: Command not found
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> It can't find the compiler.
>>>>>>>>>
>>>>>>>>> Broxton
>>>>>>>>>
>>>>>>>>> On Wed, Jun 24, 2015 at 11:31 AM, Liliana Novais <
>>>>>>>>> linovais at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hello,
>>>>>>>>>>
>>>>>>>>>> I just was able to set the core number and there is another error
>>>>>>>>>> on my installation:
>>>>>>>>>>
>>>>>>>>>> [lnovais at new-host MESA]$ ./install
>>>>>>>>>> checking if ndiff is installed ...
>>>>>>>>>> no! running install_ndiff
>>>>>>>>>> ndiff installed in utils/ndiff/
>>>>>>>>>>
>>>>>>>>>> /home/lnovais/Programs/MESA/const
>>>>>>>>>> building const package.
>>>>>>>>>>
>>>>>>>>>> gfortran -fno-range-check  -fopenmp  -I../public -I../private
>>>>>>>>>> -I../../include -Wunused-value -Werror -W -fimplicit-none   -O2 -c
>>>>>>>>>> -ffixed-form -ffixed-line-length-132 ../public/const_def.f
>>>>>>>>>> make: gfortran: Command not found
>>>>>>>>>> makefile:26: recipe for target 'const_def.o' failed
>>>>>>>>>> make: *** [const_def.o] Error 127
>>>>>>>>>>
>>>>>>>>>> /home/lnovais/Programs/MESA/const/make
>>>>>>>>>> FAILED
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> /home/lnovais/Programs/MESA/const
>>>>>>>>>> ./build_and_test FAILED
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> What is still missing?
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>> Liliana
>>>>>>>>>>
>>>>>>>>>>
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>>>>>>>>>> _______________________________________________
>>>>>>>>>> mesa-users mailing list
>>>>>>>>>> mesa-users at lists.sourceforge.net
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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