Cluster installation help

[Raghav]

Hi, 

I have been trying to use MOOSE on the Ada cluster at Texas A&M, and need some guidance with the installation process. 

The cluster has a version of MOOSE installed (MOOSE/20171003-intel-2017A-Python-2.7.12-CUDA-8.0.44). I loaded the moose module with 

>module load MOOSE

When I try to create my own app with 

>$MOOSE_DIR/scripts/stork.sh panda

I get the error messages

sed: couldn't open temporary file panda/sedMn2ukC: Permission denied

sed: couldn't open temporary file panda/sedMDJDzF: Permission denied

sed: couldn't open temporary file panda/include/base/sedDknFpI: Permission denied

mv: cannot move `panda/Makefile.app' to `panda/Makefile': Permission denied

mv: cannot move `panda/run_tests.app' to `panda/run_tests': Permission denied

mv: cannot move `panda/src/base/StorkApp.C.app' to `panda/src/base/pandaApp.C': Permission denied

mv: cannot move `panda/test/src/base/StorkTestApp.C' to `panda/test/src/base/pandaTestApp.C': Permission denied

mv: cannot move `panda/include/base/StorkApp.h' to `panda/include/base/pandaApp.h': Permission denied

mv: cannot move `panda/test/include/base/StorkTestApp.h' to `panda/test/include/base/pandaTestApp.h': Permission denied

chmod: cannot access `panda/run_tests': No such file or directory

rm: cannot remove `panda/Makefile.app': Permission denied

rm: cannot remove `panda/Makefile.module': Permission denied

rm: cannot remove `panda/run_tests.app': Permission denied

rm: cannot remove `panda/run_tests.module': Permission denied

rm: cannot remove `panda/src/base/StorkApp.C.app': Permission denied

rm: cannot remove `panda/src/base/StorkApp.C.module': Permission denied

cp: cannot create regular file `panda/.clang-format': Permission denied

cp: cannot create regular file `panda/.gitignore': Permission denied

/general/home/raghav_a/panda/.git: Permission denied

MOOSE app created in '/home/raghav_a/panda'

To store your changes on github:

    1. log in to your account

    2. Create a new repository named panda

    3. in this terminal run the following commands:

         cd /home/raghav_a/panda

         git remote add origin https://github.com/YourGitHubUserName/panda

         git commit -m "initial commit"

         git push -u origin master

To automatically enforce MOOSE C++ code style in your commits, run:

    cd /home/raghav_a/panda

    ./scripts/install-format-hook.sh

I believe that this has to do with the permissions of the $MOOSE_DIR/stork folder. 

[raghav_a@ada8 ~]$ ls -l $MOOSE_DIR/stork

total 128

dr-xr-sr-x 3 j-perdue tamusc  4096 Oct  3 08:50 include

-r--r--r-- 1 j-perdue tamusc 26530 Oct  3 08:50 LICENSE

-r--r--r-- 1 j-perdue tamusc  1965 Oct  3 08:50 Makefile.app

-r--r--r-- 1 j-perdue tamusc  1205 Oct  3 08:50 Makefile.module

-r--r--r-- 1 j-perdue tamusc   179 Oct  3 08:50 README.md

-r--r--r-- 1 j-perdue tamusc   799 Oct  3 08:50 run_tests.app

-r--r--r-- 1 j-perdue tamusc   677 Oct  3 08:50 run_tests.module

dr-xr-sr-x 2 j-perdue tamusc  4096 Oct  3 08:50 scripts

dr-xr-sr-x 3 j-perdue tamusc  4096 Oct  3 08:50 src

dr-xr-sr-x 5 j-perdue tamusc  4096 Oct  3 08:50 test

dr-xr-sr-x 4 j-perdue tamusc  4096 Oct  3 08:50 unit

To get around this, I used the stork.sh script on my local machine, and copied the new folder on to the cluster. I am not sure if this is a valid thing to do. 

I then tried to use make in the folder I copied 

> make -j4 

and got the following errors

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/libtool: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

MOOSE Compiling C++ (in opt mode) /sw/eb/software/MOOSE/20171003-intel-2017A-Python-2.7.12-CUDA-8.0.44/framework/src/actions/Action.C...

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

MOOSE Compiling C++ (in opt mode) /sw/eb/software/MOOSE/20171003-intel-2017A-Python-2.7.12-CUDA-8.0.44/framework/src/actions/ActionFactory.C...

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

/bin/sh: BROOTLIBMESH/libtool: No such file or directory

MOOSE Compiling C++ (in opt mode) /sw/eb/software/MOOSE/20171003-intel-2017A-Python-2.7.12-CUDA-8.0.44/framework/src/actions/ActionWarehouse.C...

/bin/sh: BROOTLIBMESH/contrib/bin/libmesh-config: No such file or directory

make: *** [/sw/eb/software/MOOSE/20171003-intel-2017A-Python-2.7.12-CUDA-8.0.44/framework/src/actions/Action..opt.lo] Error 127

make: *** Waiting for unfinished jobs....

/bin/sh: BROOTLIBMESH/libtool: No such file or directory

make: *** [/sw/eb/software/MOOSE/20171003-intel-2017A-Python-2.7.12-CUDA-8.0.44/framework/src/actions/ActionFactory..opt.lo] Error 127

/bin/sh: BROOTLIBMESH/libtool: No such file or directory

make: *** [/sw/eb/software/MOOSE/20171003-intel-2017A-Python-2.7.12-CUDA-8.0.44/framework/src/actions/ActionWarehouse..opt.lo] Error 127

make: *** wait: No child processes.  Stop.

I am not quite sure how to proceed from here. Any help will be appreciated. 

Thanks!

--

Raghav 

[Miller, Jason M]

On Thu, Nov 2, 2017 at 10:42 AM, Raghav <raghav...@gmail.com> wrote:

Hi, 

I have been trying to use MOOSE on the Ada cluster at Texas A&M, and need some guidance with the installation process. 

The cluster has a version of MOOSE installed (MOOSE/20171003-intel-2017A-Python-2.7.12-CUDA-8.0.44). I loaded the moose module with 

>module load MOOSE

When I try to create my own app with 

>$MOOSE_DIR/scripts/stork.sh panda

I get the error messages

sed: couldn't open temporary file panda/sedMn2ukC: Permission denied

sed: couldn't open temporary file panda/sedMDJDzF: Permission denied

sed: couldn't open temporary file panda/include/base/sedDknFpI: Permission denied

 

Looks like for some reason you did not have write access to create the necessary temp file(s) to perform the sed operation(s).

https://stackoverflow.com/questions/36404475/sed-script-permission-denied-on-temp-file

Because of this error, files were not created correctly (or at all), and thus the rest of the script failed miserably.

The permissions look fine... they are readable anyway. Which is all that is needed for stork.sh to execute properly. I was able to verify this, by removing write access to my moose directory, and the stork.sh script continued to function correctly.

Looks like a faulty LIBMESH_DIR environment variable. As panda is literally looking in a location that does not exist. Probably a LIBMESH_DIR variable being set in the "MOOSE/20171003-intel-2017A-Python-2.7.12-CUDA-8.0.44" module.

Thanks!

--

Raghav 

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Hope some of this helps!

Jason