Re: [mesa-users] Installing MESA

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Ok, I found out that running 'source /opt/mesasdk/bin/mesasdk_init.sh' is
the key to allowing the install to run properly.

However, I am still running into this problem:

/home/jared/mesa/star
building star package.

make: `libstar.a' is up to date.
make: `libstar.a' is up to date.
gfortran -fno-range-check  -fopenmp  -o ../star \
    run_star_extras.o run_star.o  run.o -L../../make -lstar -L../../../lib
-ldiffusion -lionization -latm -lcolors -lmlt -leos -lkap -lnet -lscreen
-lrates -lreaclib -lweak -lneu -lchem -linterp_2d -linterp_1d -lnum -lutils
-lalert -lconst -lmtx -lmesaklu `mesasdk_lapack_link` `mesasdk_blas_link`
`mesasdk_pgplot_link` `mesasdk_se_link`
/usr/bin/ld: cannot find -lX11
/usr/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
make: *** [star] Error 1

FAILED

/home/jared/mesa/star/test
FAILED

/home/jared/mesa/star
./build_and_test FAILED

Even though I have run the command 'export
LD_RUN_PATH=/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu' like its says
in the FAQ

-Jared

On Wed, Apr 11, 2012 at 3:22 PM, Jared Brooks <bro...@gm...>wrote:

> This time when I ran 'which gfortran' the output wasn't empty so I thought
> I would try running ./install again and it seems to be running
> successfully.  I will let you know if I run into any more problems.  Thanks
> for your help.
>
> -Jared
>
>
> On Wed, Apr 11, 2012 at 3:10 PM, Richard Townsend <tow...@as...
> > wrote:
>
>> Can you run *exactly* the following steps and send me the *exact* output:
>>
>> source /opt/mesasdk/bin/mesasdk_init.sh
>> which gfortran
>> echo $PATH
>>
>> On Apr 11, 2012, at 5:08 PM, Jared Brooks wrote:
>>
>>  jared@ubuntu:~/mesa$ ./install
>> checking if ndiff is installed ...
>> yes!
>>
>> /home/jared/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
>> make: *** [const_def.o] Error 127
>>
>> /home/jared/mesa/const/make
>> FAILED
>>
>>
>> /home/jared/mesa/const
>> ./build_and_test FAILED
>>
>> jared@ubuntu:~/mesa$ which gfortran
>> jared@ubuntu:~/mesa$ echo $MESASDK_ROOT
>> /opt/mesasdk
>> jared@ubuntu:~/mesa$ echo $PATH
>>
>> /usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
>>
>>
>> On Wed, Apr 11, 2012 at 3:02 PM, Richard Townsend <
>> tow...@as...> wrote:
>>
>>> OK, the script isn't supposed to produce any output. So, progress is
>>> being made.
>>>
>>> When you say 'the same result', do you mean the 'gfortran: Command not
>>> found error'? If so, please repeat these steps after you get the error:
>>>
>>> which gfortran
>>>
>>> echo $MESASDK_ROOT
>>>
>>> echo $PATH
>>>
>>> cheers,
>>>
>>> Rich
>>>
>>> On Apr 11, 2012, at 4:57 PM, Jared Brooks wrote:
>>>
>>> I can execute 'more mesasdk_init.sh', and I can even run the script now,
>>> but it gives no output.  Running ./install in /mesa still gives the same
>>> result.
>>>
>>> -Jared
>>>
>>> On Wed, Apr 11, 2012 at 2:52 PM, Richard Townsend <
>>> tow...@as...> wrote:
>>>
>>>> OK, thanks. Are you still unable to execute 'more mesasdk_init.sh'?
>>>>
>>>> On Apr 11, 2012, at 4:50 PM, Jared Brooks wrote:
>>>>
>>>> jared@ubuntu:/opt/mesasdk/bin$ ls -l /opt/mesasdk/bin
>>>> total 24536
>>>> -rwxr-xr-x 4 500 500 2153392 2012-01-20 09:54 c++
>>>> -rwxr-xr-x 1 500 500 2150346 2012-01-20 09:54 cpp
>>>> -rwxr-xr-x 1 500 500   77266 2012-01-20 10:03 fpx3
>>>> -rwxr-xr-x 1 500 500    2564 2012-01-20 10:03 fpx3_deps
>>>> -rwxr-xr-x 4 500 500 2153392 2012-01-20 09:54 g++
>>>> -rwxr-xr-x 3 500 500 2147774 2012-01-20 09:54 gcc
>>>> -rwxr-xr-x 2 500 500  119881 2012-01-20 09:54 gcc-ar
>>>> -rwxr-xr-x 2 500 500  119817 2012-01-20 09:54 gcc-nm
>>>> -rwxr-xr-x 2 500 500  119837 2012-01-20 09:54 gcc-ranlib
>>>> -rwxr-xr-x 1 500 500 1086658 2012-01-20 09:54 gcov
>>>> -rwxr-xr-x 2 500 500 2160578 2012-01-20 09:54 gfortran
>>>> -rwxr-xr-x 1 500 500   41082 2012-01-20 10:02 gif2h5
>>>> -rwxr-xr-x 1 500 500   38244 2012-01-20 10:02 h52gif
>>>> -rwxr-xr-x 1 500 500   12551 2012-01-20 10:02 h5cc
>>>> -rwxr-xr-x 1 500 500  112948 2012-01-20 10:02 h5copy
>>>> -rwxr-xr-x 1 500 500   19590 2012-01-20 10:02 h5debug
>>>> -rwxr-xr-x 1 500 500  229329 2012-01-20 10:02 h5diff
>>>> -rwxr-xr-x 1 500 500  197313 2012-01-20 10:02 h5dump
>>>> -rwxr-xr-x 1 500 500   11693 2012-01-20 10:02 h5fc
>>>> -rwxr-xr-x 1 500 500   79908 2012-01-20 10:02 h5import
>>>> -rwxr-xr-x 1 500 500   35368 2012-01-20 10:02 h5jam
>>>> -rwxr-xr-x 1 500 500  141757 2012-01-20 10:02 h5ls
>>>> -rwxr-xr-x 1 500 500  111278 2012-01-20 10:02 h5mkgrp
>>>> -rwxr-xr-x 1 500 500   69706 2012-01-20 10:02 h5perf_serial
>>>> -rwxr-xr-x 1 500 500    4434 2012-01-20 10:02 h5redeploy
>>>> -rwxr-xr-x 1 500 500  169697 2012-01-20 10:02 h5repack
>>>> -rwxr-xr-x 1 500 500   15639 2012-01-20 10:02 h5repart
>>>> -rwxr-xr-x 1 500 500  122193 2012-01-20 10:02 h5stat
>>>> -rwxr-xr-x 1 500 500   32235 2012-01-20 10:02 h5unjam
>>>> -rwxr-xr-x 1 500 500    1137 2012-01-20 10:03 mesasdk_arch_check.pl
>>>> -rwxr-xr-x 1 500 500      71 2012-01-20 09:55 mesasdk_blas_link
>>>> -rwxr-xr-x 1 500 500      89 2012-01-20 10:03 mesasdk_hdf5_link
>>>> -rwxr-xr-x 1 500 500     835 2012-01-20 10:03 mesasdk_init.csh
>>>> -rwxr-xr-x 1 500 500     611 2012-01-20 10:03 mesasdk_init.sh
>>>> -rwxr-xr-x 1 500 500     101 2012-01-20 09:58 mesasdk_lapack95_link
>>>> -rwxr-xr-x 1 500 500      95 2012-01-20 09:56 mesasdk_lapack_link
>>>> -rwxr-xr-x 1 500 500      83 2012-01-20 09:58 mesasdk_pgplot_link
>>>> -rwxr-xr-x 1 500 500      86 2012-01-20 10:03 mesasdk_se_link
>>>> -rwxr-xr-x 2 500 500   42426 2012-01-20 10:03 ndiff
>>>> -rwxr-xr-x 2 500 500   42426 2012-01-20 10:03 ndiff-2.00
>>>> -rwxr-xr-x 1 500 500   12512 2012-01-20 10:03 touchse
>>>> -rwxr-xr-x 4 500 500 2153392 2012-01-20 09:54 x86_64-pc-linux-gnu-c++
>>>> -rwxr-xr-x 4 500 500 2153392 2012-01-20 09:54 x86_64-pc-linux-gnu-g++
>>>> -rwxr-xr-x 3 500 500 2147774 2012-01-20 09:54 x86_64-pc-linux-gnu-gcc
>>>> -rwxr-xr-x 3 500 500 2147774 2012-01-20 09:54
>>>> x86_64-pc-linux-gnu-gcc-4.7.0
>>>> -rwxr-xr-x 2 500 500  119881 2012-01-20 09:54 x86_64-pc-linux-gnu-gcc-ar
>>>> -rwxr-xr-x 2 500 500  119817 2012-01-20 09:54 x86_64-pc-linux-gnu-gcc-nm
>>>> -rwxr-xr-x 2 500 500  119837 2012-01-20 09:54
>>>> x86_64-pc-linux-gnu-gcc-ranlib
>>>> -rwxr-xr-x 2 500 500 2160578 2012-01-20 09:54
>>>> x86_64-pc-linux-gnu-gfortran
>>>>
>>>>
>>>> Here's the file I unpacked into /opt:
>>>> mesasdk-x86_64-linux-20120120.tar.gz
>>>>
>>>>
>>>> On Wed, Apr 11, 2012 at 2:48 PM, Richard Townsend <
>>>> tow...@as...> wrote:
>>>>
>>>>> Please could you send the new 'ls -l', and also let me know the actual
>>>>> name of the file you unpacked into /opt.
>>>>>
>>>>> cheers,
>>>>>
>>>>> Rich
>>>>>
>>>>> On Apr 11, 2012, at 4:46 PM, Jared Brooks wrote:
>>>>>
>>>>> I changed those permissions, and those changes were reflected by a ls
>>>>> -l, but it is still denying me permission.
>>>>>
>>>>> I downloaded the Linux 64 bit SDK from this page:
>>>>> http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk
>>>>>
>>>>> -Jared
>>>>>
>>>>> On Wed, Apr 11, 2012 at 2:37 PM, Richard Townsend <
>>>>> tow...@as...> wrote:
>>>>>
>>>>>> As root user, execute the following:
>>>>>>
>>>>>> chmod 755 /opt/mesasdk/bin/mesasdk_init.csh
>>>>>> chmod 755 /opt/mesasdk/bin/mesasdk_init.sh
>>>>>>
>>>>>> I'm not sure what led to this problem; what version of the SDK are
>>>>>> you using (i.e., what file did you download)?
>>>>>>
>>>>>> cheers,
>>>>>>
>>>>>> Rich
>>>>>>
>>>>>> On Apr 11, 2012, at 4:34 PM, Jared Brooks wrote:
>>>>>>
>>>>>> jared@ubuntu:/opt/mesasdk/bin$ ls -l /opt/mesasdk/bin
>>>>>> total 24536
>>>>>> -rwxr-xr-x 4 500 500 2153392 2012-01-20 09:54 c++
>>>>>> -rwxr-xr-x 1 500 500 2150346 2012-01-20 09:54 cpp
>>>>>> -rwxr-xr-x 1 500 500   77266 2012-01-20 10:03 fpx3
>>>>>> -rwxr-xr-x 1 500 500    2564 2012-01-20 10:03 fpx3_deps
>>>>>> -rwxr-xr-x 4 500 500 2153392 2012-01-20 09:54 g++
>>>>>> -rwxr-xr-x 3 500 500 2147774 2012-01-20 09:54 gcc
>>>>>> -rwxr-xr-x 2 500 500  119881 2012-01-20 09:54 gcc-ar
>>>>>> -rwxr-xr-x 2 500 500  119817 2012-01-20 09:54 gcc-nm
>>>>>> -rwxr-xr-x 2 500 500  119837 2012-01-20 09:54 gcc-ranlib
>>>>>> -rwxr-xr-x 1 500 500 1086658 2012-01-20 09:54 gcov
>>>>>> -rwxr-xr-x 2 500 500 2160578 2012-01-20 09:54 gfortran
>>>>>> -rwxr-xr-x 1 500 500   41082 2012-01-20 10:02 gif2h5
>>>>>> -rwxr-xr-x 1 500 500   38244 2012-01-20 10:02 h52gif
>>>>>> -rwxr-xr-x 1 500 500   12551 2012-01-20 10:02 h5cc
>>>>>> -rwxr-xr-x 1 500 500  112948 2012-01-20 10:02 h5copy
>>>>>> -rwxr-xr-x 1 500 500   19590 2012-01-20 10:02 h5debug
>>>>>> -rwxr-xr-x 1 500 500  229329 2012-01-20 10:02 h5diff
>>>>>> -rwxr-xr-x 1 500 500  197313 2012-01-20 10:02 h5dump
>>>>>> -rwxr-xr-x 1 500 500   11693 2012-01-20 10:02 h5fc
>>>>>> -rwxr-xr-x 1 500 500   79908 2012-01-20 10:02 h5import
>>>>>> -rwxr-xr-x 1 500 500   35368 2012-01-20 10:02 h5jam
>>>>>> -rwxr-xr-x 1 500 500  141757 2012-01-20 10:02 h5ls
>>>>>> -rwxr-xr-x 1 500 500  111278 2012-01-20 10:02 h5mkgrp
>>>>>> -rwxr-xr-x 1 500 500   69706 2012-01-20 10:02 h5perf_serial
>>>>>> -rwxr-xr-x 1 500 500    4434 2012-01-20 10:02 h5redeploy
>>>>>> -rwxr-xr-x 1 500 500  169697 2012-01-20 10:02 h5repack
>>>>>> -rwxr-xr-x 1 500 500   15639 2012-01-20 10:02 h5repart
>>>>>> -rwxr-xr-x 1 500 500  122193 2012-01-20 10:02 h5stat
>>>>>> -rwxr-xr-x 1 500 500   32235 2012-01-20 10:02 h5unjam
>>>>>> -rwxr-xr-x 1 500 500    1137 2012-01-20 10:03 mesasdk_arch_check.pl
>>>>>> -rwxr-xr-x 1 500 500      71 2012-01-20 09:55 mesasdk_blas_link
>>>>>> -rwxr-xr-x 1 500 500      89 2012-01-20 10:03 mesasdk_hdf5_link
>>>>>> -rwxrwx--- 1 500 500     835 2012-01-20 10:03 mesasdk_init.csh
>>>>>> -rwxrwx--- 1 500 500     611 2012-01-20 10:03 mesasdk_init.sh
>>>>>> -rwxr-xr-x 1 500 500     101 2012-01-20 09:58 mesasdk_lapack95_link
>>>>>> -rwxr-xr-x 1 500 500      95 2012-01-20 09:56 mesasdk_lapack_link
>>>>>> -rwxr-xr-x 1 500 500      83 2012-01-20 09:58 mesasdk_pgplot_link
>>>>>> -rwxr-xr-x 1 500 500      86 2012-01-20 10:03 mesasdk_se_link
>>>>>> -rwxr-xr-x 2 500 500   42426 2012-01-20 10:03 ndiff
>>>>>> -rwxr-xr-x 2 500 500   42426 2012-01-20 10:03 ndiff-2.00
>>>>>> -rwxr-xr-x 1 500 500   12512 2012-01-20 10:03 touchse
>>>>>> -rwxr-xr-x 4 500 500 2153392 2012-01-20 09:54 x86_64-pc-linux-gnu-c++
>>>>>> -rwxr-xr-x 4 500 500 2153392 2012-01-20 09:54 x86_64-pc-linux-gnu-g++
>>>>>> -rwxr-xr-x 3 500 500 2147774 2012-01-20 09:54 x86_64-pc-linux-gnu-gcc
>>>>>> -rwxr-xr-x 3 500 500 2147774 2012-01-20 09:54
>>>>>> x86_64-pc-linux-gnu-gcc-4.7.0
>>>>>> -rwxr-xr-x 2 500 500  119881 2012-01-20 09:54
>>>>>> x86_64-pc-linux-gnu-gcc-ar
>>>>>> -rwxr-xr-x 2 500 500  119817 2012-01-20 09:54
>>>>>> x86_64-pc-linux-gnu-gcc-nm
>>>>>> -rwxr-xr-x 2 500 500  119837 2012-01-20 09:54
>>>>>> x86_64-pc-linux-gnu-gcc-ranlib
>>>>>> -rwxr-xr-x 2 500 500 2160578 2012-01-20 09:54
>>>>>> x86_64-pc-linux-gnu-gfortran
>>>>>> jared@ubuntu:/opt/mesasdk/bin$ more mesasdk_init.sh
>>>>>> mesasdk_init.sh: Permission denied
>>>>>>
>>>>>> It looks like I should be able to access all these files, but for
>>>>>> some reason it's still keeping me out
>>>>>>
>>>>>> -Jared
>>>>>>
>>>>>>
>>>>>> On Wed, Apr 11, 2012 at 2:30 PM, Richard Townsend <
>>>>>> tow...@as...> wrote:
>>>>>>
>>>>>>> Could you post the output from 'ls -l /opt/mesasdk/bin'. That will
>>>>>>> show what permission problems may exist.
>>>>>>>
>>>>>>> On Apr 11, 2012, at 4:27 PM, Jared Brooks wrote:
>>>>>>>
>>>>>>> Here's a command I found concerning PATH in my .profile:
>>>>>>>
>>>>>>> # set PATH so it includes user's private bin if it exists
>>>>>>> if [ -d "$HOME/bin" ] ; then
>>>>>>>     PATH="$HOME/bin:$PATH"
>>>>>>> fi
>>>>>>>
>>>>>>> And here's the output to that source command:
>>>>>>>
>>>>>>> jared@ubuntu:~/mesa$ source $MESASDK_ROOT/bin/mesasdk_init.sh
>>>>>>> bash: /opt/mesasdk/bin/mesasdk_init.sh: Permission denied
>>>>>>>
>>>>>>> I've had a hunch that permissions were at the source of my problems,
>>>>>>> but I still don't understand why it's keeping me out.
>>>>>>>
>>>>>>> -Jared
>>>>>>>
>>>>>>> On Wed, Apr 11, 2012 at 2:20 PM, Richard Townsend <
>>>>>>> tow...@as...> wrote:
>>>>>>>
>>>>>>>> OK, thanks. Please post the output when you run
>>>>>>>>
>>>>>>>> source $MESASDK_ROOT/bin/mesasdk_init.sh
>>>>>>>>
>>>>>>>> Also, please confirm that you don't have anything else in your
>>>>>>>> .profile startup script which overwrites the PATH environment variable.
>>>>>>>>
>>>>>>>> cheers,
>>>>>>>>
>>>>>>>> Rich
>>>>>>>>
>>>>>>>> On Apr 11, 2012, at 4:17 PM, Jared Brooks wrote:
>>>>>>>>
>>>>>>>> jared@ubuntu:~/mesa$ which gfortran
>>>>>>>> jared@ubuntu:~/mesa$ echo $MESASDK_ROOT
>>>>>>>> /opt/mesasdk
>>>>>>>> jared@ubuntu:~/mesa$ echo $PATH
>>>>>>>>
>>>>>>>> /usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
>>>>>>>>
>>>>>>>> -Jared
>>>>>>>>
>>>>>>>> On Wed, Apr 11, 2012 at 2:14 PM, Richard Townsend <
>>>>>>>> tow...@as...> wrote:
>>>>>>>>
>>>>>>>>> After you get the 'make: gfortran: Command not found', please run
>>>>>>>>> the following commands and post the output:
>>>>>>>>>
>>>>>>>>> which gfortran
>>>>>>>>>
>>>>>>>>> echo $MESASDK_ROOT
>>>>>>>>>
>>>>>>>>> echo $PATH
>>>>>>>>>
>>>>>>>>> cheers,
>>>>>>>>>
>>>>>>>>> Rich
>>>>>>>>>
>>>>>>>>> On Apr 11, 2012, at 4:10 PM, Jared Brooks wrote:
>>>>>>>>>
>>>>>>>>> I have had these commands in my .profile
>>>>>>>>>
>>>>>>>>> export MESASDK_ROOT=/opt/mesasdk
>>>>>>>>> source $MESASDK_ROOT/bin/mesasdk_init.sh
>>>>>>>>> export OMP_NUM_THREADS=4
>>>>>>>>> export LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
>>>>>>>>> export LD_RUN_PATH=/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu
>>>>>>>>>
>>>>>>>>> -Jared
>>>>>>>>>
>>>>>>>>> On Wed, Apr 11, 2012 at 1:53 PM, Richard Townsend <
>>>>>>>>> tow...@as...> wrote:
>>>>>>>>>
>>>>>>>>>> Have you initialized the SDK properly using the appropriate
>>>>>>>>>> script? You have to do this each time you log in -- or add a line to your
>>>>>>>>>> start-up file (.cshrc, .bashrc, etc.)
>>>>>>>>>>
>>>>>>>>>> On Apr 11, 2012, at 3:33 PM, Jared Brooks wrote:
>>>>>>>>>>
>>>>>>>>>> > Hello, I'm running Ubuntu and I can't get MESA installed
>>>>>>>>>> completely.  I'm using the MESA_SDK and I followed the FAQ, yet I'm still
>>>>>>>>>> stuck.  I got the install script to run for a few hours before it stopped
>>>>>>>>>> and now will only give me this:
>>>>>>>>>> >
>>>>>>>>>> > jared@ubuntu:~/mesa$ ./install
>>>>>>>>>> > checking if ndiff is installed ...
>>>>>>>>>> > yes!
>>>>>>>>>> >
>>>>>>>>>> > /home/jared/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
>>>>>>>>>> > make: *** [const_def.o] Error 127
>>>>>>>>>> >
>>>>>>>>>> > /home/jared/mesa/const/make
>>>>>>>>>> > FAILED
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> > /home/jared/mesa/const
>>>>>>>>>> > ./build_and_test FAILED
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> > And I found this message in the file mesa/const/test/tmp.txt:
>>>>>>>>>> >
>>>>>>>>>> > ./tester: error while loading shared libraries:
>>>>>>>>>> libgfortran.so.3: cannot open shared object file: No such file or directory
>>>>>>>>>> >
>>>>>>>>>> > I found the file libgfortran.so.3 in /opt/mesasdk/lib64/, it
>>>>>>>>>> seems to be just a pointer to libgfortran.so.3.0.0.
>>>>>>>>>> >
>>>>>>>>>> > -Jared
>>>>>>>>>> >
>>>>>>>>>> ------------------------------------------------------------------------------
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>>>>>>>>>> http://p.sf.net/sfu/Boundary-dev2dev_______________________________________________
>>>>>>>>>> > mesa-users mailing list
>>>>>>>>>> > mes...@li...
>>>>>>>>>> > https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
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>