[mesa-users] Installing MESA

Richard Townsend townsend at astro.wisc.edu
Wed Apr 11 20:06:11 EDT 2012 

Have you installed the X windows library (libx11-dev on Ubuntu), as specified in the prerequisites listed on the web page?

You'll also have to install the Z library (libz-dev on Ubuntu).

On Apr 11, 2012, at 7:01 PM, Jared Brooks wrote:

> 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 <brooksjaredc at gmail.com> 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 <townsend at astro.wisc.edu> wrote:
> Can you run *exactly* the following steps and send me the *exact* output:
> 
> source /opt/mesasdk/bin/mesasdk_init.sh
> which gfortran
> echo $PATH
> 
> On Apr 11, 2012, at 5:08 PM, Jared Brooks wrote:
> 
>>  jared at ubuntu:~/mesa$ ./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 at ubuntu:~/mesa$ which gfortran
>> jared at ubuntu:~/mesa$ echo $MESASDK_ROOT
>> /opt/mesasdk
>> jared at ubuntu:~/mesa$ 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 <townsend at astro.wisc.edu> 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 $PATH
>> 
>> cheers,
>> 
>> Rich
>> 
>> On Apr 11, 2012, at 4:57 PM, Jared Brooks wrote:
>> 
>>> I can execute 'more mesasdk_init.sh', and I can even run the script now, but it gives no output.  Running ./install in /mesa still gives the same result.
>>> 
>>> -Jared
>>> 
>>> On Wed, Apr 11, 2012 at 2:52 PM, Richard Townsend <townsend at astro.wisc.edu> wrote:
>>> OK, thanks. Are you still unable to execute 'more mesasdk_init.sh'?
>>> 
>>> On Apr 11, 2012, at 4:50 PM, Jared Brooks wrote:
>>> 
>>>> jared at ubuntu:/opt/mesasdk/bin$ 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 <townsend at astro.wisc.edu> 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 <townsend at astro.wisc.edu> 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 at 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 at 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 <townsend at astro.wisc.edu> 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:$PATH"
>>>>>>> fi
>>>>>>> 
>>>>>>> And here's the output to that source command:
>>>>>>> 
>>>>>>> jared at ubuntu:~/mesa$ 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 <townsend at astro.wisc.edu> wrote:
>>>>>>> OK, thanks. Please post the output when you run
>>>>>>> 
>>>>>>> source $MESASDK_ROOT/bin/mesasdk_init.sh
>>>>>>> 
>>>>>>> Also, please confirm that you don't have anything else in your .profile startup script which overwrites the PATH environment variable.
>>>>>>> 
>>>>>>> cheers,
>>>>>>> 
>>>>>>> Rich
>>>>>>> 
>>>>>>> On Apr 11, 2012, at 4:17 PM, Jared Brooks wrote:
>>>>>>> 
>>>>>>>> jared at ubuntu:~/mesa$ which gfortran
>>>>>>>> jared at ubuntu:~/mesa$ echo $MESASDK_ROOT
>>>>>>>> /opt/mesasdk
>>>>>>>> jared at ubuntu:~/mesa$ 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 <townsend at astro.wisc.edu> 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 $MESASDK_ROOT/bin/mesasdk_init.sh
>>>>>>>>> export OMP_NUM_THREADS=4
>>>>>>>>> export LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
>>>>>>>>> export LD_RUN_PATH=/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu
>>>>>>>>> 
>>>>>>>>> -Jared
>>>>>>>>> 
>>>>>>>>> On Wed, Apr 11, 2012 at 1:53 PM, Richard Townsend <townsend at astro.wisc.edu> wrote:
>>>>>>>>> Have you initialized the SDK properly using the appropriate script? You have to do this each time you log in -- or add a line to your start-up file (.cshrc, .bashrc, etc.)
>>>>>>>>> 
>>>>>>>>> On Apr 11, 2012, at 3:33 PM, Jared Brooks wrote:
>>>>>>>>> 
>>>>>>>>> > Hello, I'm running Ubuntu and I can't get MESA installed completely.  I'm using the MESA_SDK and I followed the FAQ, yet I'm still stuck.  I got the install script to run for a few hours before it stopped and now will only give me this:
>>>>>>>>> >
>>>>>>>>> > jared at ubuntu:~/mesa$ ./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
>>>>>>>>> > ------------------------------------------------------------------------------
>>>>>>>>> > Better than sec? Nothing is better than sec when it comes to
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>>>>>>>>> > http://p.sf.net/sfu/Boundary-dev2dev_______________________________________________
>>>>>>>>> > mesa-users mailing list
>>>>>>>>> > mesa-users at lists.sourceforge.net
>>>>>>>>> > https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
> 
> 
> 

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