Installation of MOFEM on a secure server: Issue with curl

[lmaku...@gmail.com]

Hi Everyone,

I'm currently trying to install mofem on a secure server using spack mirror.

spack mirror add local_MOFEM file://$HOME/spack-mirror-2018-11-02

Then going back to the installation phase:

- . spack/share/spack/setup-env.sh ==> OK

- spack bootstrap

==> Requirement environment-modules is satisfied with installed package environme...@3.2.10%g...@4.9.2~X arch=linux-debian8-x86_64  ^t...@8.6.8%g...@4.9.2 arch=linux-debian8-x86_64  ^zl...@1.2.11%g...@4.9.2+optimize+pic+shared arch=linux-debian8-x86_64

. ${SPACK_ROOT}/share/spack/setup-env.sh ==> OK

- spack install -j 8 gcc ==> I'm getting this error

==> Installing isl
==> Fetching file://opt/spack-mirror-2018-07-26/isl/isl-0.19.tar.bz2
curl: (37) Couldn't open file /spack-mirror-2018-07-26/isl/isl-0.19.tar.bz2
==> Fetching from file://opt/spack-mirror-2018-07-26/isl/isl-0.19.tar.bz2 failed.
==> Fetching file:///home/B87457/spack-mirror-2018-11-02/isl/isl-0.19.tar.bz2
curl: (37) Couldn't open file /home/B87457/spack-mirror-2018-11-02/isl/isl-0.19.tar.bz2
==> Fetching from file:///home/B87457/spack-mirror-2018-11-02/isl/isl-0.19.tar.bz2 failed.
==> Fetching http://isl.gforge.inria.fr/isl-0.19.tar.bz2

curl: (7) Failed to connect to isl.gforge.inria.fr port 80: Connexion refusée
==> Fetching from http://isl.gforge.inria.fr/isl-0.19.tar.bz2 failed.
==> Error: FetchError: All fetchers failed for isl-0.19-tevnb62xd4muk6u3ioxhuspube75q4mf

/gpfseole/home/B87457/mofem/install_mofem/spack-develop/lib/spack/spack/package.py:934, in do_fetch:
        931                raise FetchError("Will not fetch %s" %
        932                                 self.spec.format('$_$@'), ck_msg)
        933
  >>    934        self.stage.create()
        935        self.stage.fetch(mirror_only)
        936        self._fetch_time = time.time() - start_time
        937

Can someone could help me please ?

Dzifa Kudawoo,

EDF Energy

 

[Karol Lewandowski]

Hi,

you have to create your own mirror that will contain all those packages you need. On a computer with normal internet install spack and run:

spack mirror create -D gcc

It will generate a folder spack-mirror-2018-11-02 (name depending on the date). Next you can add more packages to that mirror, necessary to install mofem, for example:

spack mirror create -D mofem-fracture-module
spack mirror create -D curl

They will also fetch all the dependencies. 

Next you have to copy that folder to your secure server and add it like:

spack mirror add local_filesystem_mofem file://$HOME/spack-mirror-2018-11-02 #location of your mirror

When you execute 'spack install -j 8 gcc ' it will fetch the data from your mirror and the package should install normally.

Let me know if you have any problems.

[Dzifa Kudawoo]

Many thanks Karol for your reply,

I've completed the steps you describe and it seems that "spack install -j 8 gcc" is not getting the same error as previously reported.

The installation of gcc takes a while and I'll let you know as soon as possible.Is that normal ?

"""
==> Installing gcc>

.....

==> Executing phase: 'autoreconf'
==> Executing phase: 'configure'
==> Executing phase: 'build'
"""

[Dzifa Kudawoo]

The complete question is: Is that normal that it takes a long time ?

[Karol Lewandowski]

Yes, it can take hours, depending on the machine.

[Dzifa Kudawoo]

Right, everything is ploding along then.

I'll let you know if the installation is finished. I guess that the following steps are:

"""

spack load gcc

spack compiler find

spack install -j 8 curl

spack load curl

spack install -j 8 mofem-users-modules%g...@8.1.0

"""

[Dzifa Kudawoo]

Me again,

When I execute the command: spack install -j 8 mofem-users-modules%g...@8.1.0, I'm getting an error

==> Error: No compilers with spec g...@8.1.0 found
Run 'spack compiler find' to add compilers.

Obviously, I ran spack compiler find
==> Found no new compilers
==> Compilers are defined in the following files:
    /home/B87457/.spack/linux/compilers.yaml

What can I do ?

[Dzifa Kudawoo]

I change 8.1.0 ==> 8.2.0 after looking at """/home/B87457/.spack/linux/compilers.yaml""". Is it the good thing to do ?

It seems to run.

[Karol Lewandowski]

Did you run?

spack load gcc

It seems that there was some issue with the version, spack issue.

[Dzifa Kudawoo]

Yes

[Dzifa Kudawoo]

I report here some issue that I solve in hand:

#################### Issue1: gcc#########################

spack install -j 8 mofem-users-modules%g...@8.1.0, I'm getting an error

==> Error: No compilers with spec g...@8.1.0 found
Run 'spack compiler find' to add compilers.

When I replace by g...@8.1.0 by g...@8.2.0 after looking in compilers.yaml file It works fine

####################Issue2: boost########################

 Installing boost
==> Fetching file://opt/spack-mirror-2018-07-26/boost/boost-1.68.0.tar.bz2
curl: (3) Invalid file://hostname/, expected localhost or 127.0.0.1 or none
==> Fetching from file://opt/spack-mirror-2018-07-26/boost/boost-1.68.0.tar.bz2 failed.
==> Fetching file:///home/B87457/spack-mirror-2018-11-02/boost/boost-1.68.0.tar.bz2
curl: (37) Couldn't open file /home/B87457/spack-mirror-2018-11-02/boost/boost-1.68.0.tar.bz2
==> Fetching from file:///home/B87457/spack-mirror-2018-11-02/boost/boost-1.68.0.tar.bz2 failed.
==> Fetching file:///home/B87457/spack-mirror-2018-07-21/boost/boost-1.68.0.tar.bz2
curl: (37) Couldn't open file /home/B87457/spack-mirror-2018-07-21/boost/boost-1.68.0.tar.bz2
==> Fetching from file:///home/B87457/spack-mirror-2018-07-21/boost/boost-1.68.0.tar.bz2 failed.
==> Fetching file://home/B87457/spack-mirror-2018-11-02/boost/boost-1.68.0.tar.bz2
curl: (3) Invalid file://hostname/, expected localhost or 127.0.0.1 or none
==> Fetching from file://home/B87457/spack-mirror-2018-11-02/boost/boost-1.68.0.tar.bz2 failed.
==> Fetching https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.bz2
-#O=#     #       #
curl: (7) Failed to connect to dl.bintray.com port 443: Connexion refusée
==> Fetching from https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.bz2 failed.
==> Cannot find version 1.68.0 in url_list
==> Error: FetchError: All fetchers failed for boost-1.68.0-e3x75qcmsgepnaykhwvtl6caknq5u6xc

/gpfseole/home/B87457/mofem/install_mofem/spack-develop/lib/spack/spack/package.py:934, in do_fetch:
        931                raise FetchError("Will not fetch %s" %
        932                                 self.spec.format('$_$@'), ck_msg)
        933
  >>    934        self.stage.create()
        935        self.stage.fetch(mirror_only)
        936        self._fetch_time = time.time() - start_time

When I fetch my mirror, I had boost-1.67.0.tar.bz2 but not boost-1.68.0.tar.bz2. Then I dowload the boost-1.68.0.tar.bz2 file by hand end then copy it in the mirror.

It works and the installation is going on.

[Dzifa Kudawoo]

I meet now an Issue regarding MOAB installation. Is someone can hep me fix it ?

==> Installing moab
==> Using cached archive: /gpfseole/home/B87457/mofem/install_mofem/spack-develop/var/spack/cache/moab/moab-5.0.2.tar.gz
==> Staging archive: /gpfseole/home/B87457/mofem/install_mofem/spack-develop/var/spack/stage/moab-5.0.2-m7eydvz7lzyuxvqbepidxk4edtam3v44/moab-5.0.2.tar.gz
==> Created stage in /gpfseole/home/B87457/mofem/install_mofem/spack-develop/var/spack/stage/moab-5.0.2-m7eydvz7lzyuxvqbepidxk4edtam3v44
==> No patches needed for moab
==> Building moab [AutotoolsPackage]

==> Executing phase: 'autoreconf'
==> Executing phase: 'configure'
==> Executing phase: 'build'

==> Error: ProcessError: Command exited with status 2:
    'make' '-j8'

77 errors found in build log:
     2954      CXX      WriteVtk.lo
     2955      CXX      ReadCGNS.lo
     2956      CXX      WriteCGNS.lo
     2957      CXX      HDF5Common.lo
     2958      CXX      ReadHDF5.lo
     2959    ReadCGNS.cpp: Dans la fonction membre « virtual moab::ErrorCode moab::ReadCGNS::load_file(const char*, const EntityHandle*, const moab::FileOptions&, const moab::ReaderIface::SubsetL
             ist*, moab::TagInfo* const*) »:
  >> 2960    ReadCGNS.cpp:164:21: error: « RealDouble » n'a pas été déclaré dans cette portée
     2961                         RealDouble, &beginPos, &endPos, coord_arrays[0]);
     2962                         ^~~~~~~~~~
     2963    ReadCGNS.cpp:164:21: note: alternatives suggérées: « CG_RealDouble »
     2964                         RealDouble, &beginPos, &endPos, coord_arrays[0]);
     2965                         ^~~~~~~~~~
     2966                         CG_RealDouble
     2967    In file included from WriteCGNS.cpp:1:
  >> 2968    WriteCGNS.hpp:33:4: error: #error enumeration scoping needs to be off
     2969     #  error enumeration scoping needs to be off
     2970        ^~~~~
  >> 2971    ReadCGNS.cpp:218:9: error: « ElementType_t » n'a pas été déclaré dans cette portée

[Karol Lewandowski]

what is the output when you run

which gcc

?

[Dzifa Kudawoo]

/gpfseole/home/B87457/mofem/install_mofem/spack-develop/opt/spack/linux-debian8-x86_64/gcc-5.2.0/gcc-8.2.0-n5lcjoo5ircgd7tyy7wzghac5pjtas4q/bin/gcc

[Karol Lewandowski]

I've never had this problem. I think only Lukasz can help here. One more shot. Try

printf "config: \n     build_jobs: 4" >> $HOME/.spack/config.yaml

and run install mofem-users-modules again.

[Dzifa Kudawoo]

this is the same error.

May be I could restart from scratch. How can I clean properly the installed packages ? Is ther a spack clean command ?

[Karol Lewandowski]

I don't think it could help. I was installing mofem with exactly the same compiler and the same version of moab several times.
How did you download spack? 

Did you use this repo? 

git clone --single-branch -b mofem https://github.com/likask/spack.git

Maybe boost is causing problems. I've always used bo...@1.67.0. I am not sure why yours required 1.68.0

try 

spack uninstall boost@1.68.0

and then

spack install mofem-users-modules@develop

[Lukasz Kaczmraczyk]

Hello,

The problem is that MOAB pick-up stuff installed in your system, i.e. CGNS. And compilation reader for CGNS is a source of the problem.  Can you tell where you have it located on the server?

1) To resinsrall, the best is to delate spack directory, clone it again, and start process from beginning. 

2) You do not have to load and install curl, anyway you don't have access to external world.

3) Can you tell what linux you have on the cluster?

Kind regards,

Lukasz

[Lukasz Kaczmraczyk]

Hello Dzifa and Karol,

CGSN is compiled with other compilers, native to your system. It could be that I will have to put fix to the configuration of Moab with Spack.  Could you please reinstall spack again, one once you get the same problem I will try to send fix to resolve the problem.

Kind regards,

Lukasz

[Lukasz Kaczmraczyk]

Hello Dzifa and Karol,

I made fix to moab install in spack, switching off compilation with cgsn. Pleas pull spack again, and this should work.

Regards,

Lukasz

[Dzifa Kudawoo]

Hi everyone,

I'm back in the business. Thank for all your answers and I really appreciate the support.

Lukasz it is a good thing to disable the cgsn option. I am about to start now the installation from scratch on an EDF cluster.

I follow this steps:

1. Since, I cannot use git to clone the spack repo: https://github.com/likask/spack.git


I choose to download it by hand and copy it in the cluster machine. Another way is to


git clone --single-branch -b mofem https://github.com/likask/spack.git




the repo on a local machine and copy the folder to the cluster machine. I stuck in the first option for the moment. Any advice ?





2. Creation of a mirror:

I follow the steps advised by Karol.

spack mirror create -D gcc

Then I add the packages that I need to install mofem properly


spack mirror create -D mofem-fracture-module
spack mirror create -D curl




Any package miss ? (Boost, ... perl, ... etc )





Results: While performing "spack mirror create -D mofem-fracture-module", I get this result:

==> Successfully updated mirror in spack-mirror-2018-11-05
  Archive stats:
    11   already present
    28   added
    1    failed to fetch.
==> Error: Failed downloads:
mofem-frac...@0.9.48


Is that mean It is good ?








3. Start from the begining

When trying to setup the environment I've got this error.

Traceback (most recent call last):
  File "/home/B87457/mofem/install_dir/spack/bin/spack", line 54, in <module>
    sys.exit(spack.main.main())
  File "/gpfseole/home/B87457/mofem/install_dir/spack/lib/spack/spack/main.py", line 600, in main
    print_setup_info(*args.print_shell_vars.split(','))
  File "/gpfseole/home/B87457/mofem/install_dir/spack/lib/spack/spack/main.py", line 565, in print_setup_info
    module_roots = spack.config.get('config:module_roots')
  File "/gpfseole/home/B87457/mofem/install_dir/spack/lib/spack/spack/config.py", line 573, in get
    return config.get(path, default, scope)
  File "/gpfseole/home/B87457/mofem/install_dir/spack/lib/spack/spack/config.py", line 423, in get
    value = self.get_config(section, scope=scope)
  File "/gpfseole/home/B87457/mofem/install_dir/spack/lib/spack/spack/config.py", line 388, in get_config
    data = scope.get_section(section)
  File "/gpfseole/home/B87457/mofem/install_dir/spack/lib/spack/spack/config.py", line 187, in get_section
    data   = _read_config_file(path, schema)
  File "/gpfseole/home/B87457/mofem/install_dir/spack/lib/spack/spack/config.py", line 640, in _read_config_file
    "Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
spack.config.ConfigFileError: Error parsing yamlNone: mapping values are not allowed here


Any advice ?








[Karol Lewandowski]

Are you installing from scratch on the same server?

Then you should also delete the following folder:

rm -rf $HOME/.spack

But then the entire configure is lost and you would have to add the mirror again:

spack add local_ etc..

[Dzifa Kudawoo]

Done thanks!

[Dzifa Kudawoo]

Hi all a quick update:

With the command:

"""

spack install -j 8 mofem-users-modules%g...@8.1.0

"""

I've got this error:

==> Error: No compilers with spec g...@8.1.0 found
Run 'spack compiler find' to add compilers.

I'm pretty sure that I have the 8.2.0 then when trying

"""

spack install -j 8 mofem-users-modules%g...@8.2.0

"""

I've got this error:

==> Installing petsc
==> Using cached archive: /gpfseole/home/B87457/mofem/install_dir/spack/var/spack/cache/petsc/petsc-3.9.3.tar.gz
==> Staging archive: /gpfseole/home/B87457/mofem/install_dir/spack/var/spack/stage/petsc-3.9.3-bsj7hkkbzmf7tseye7ixyjcrx6yz2rcg/petsc-3.9.3.tar.gz
==> Created stage in /gpfseole/home/B87457/mofem/install_dir/spack/var/spack/stage/petsc-3.9.3-bsj7hkkbzmf7tseye7ixyjcrx6yz2rcg
==> No patches needed for petsc
==> Building petsc [Package]
==> Executing phase: 'install'

==> Error: ProcessError: Command exited with status 2:

    'make' 'MAKE_NP=8'

3 errors found in build log:
     1990              FC arch-linux2-c-opt/obj/dm/f90-mod/petscdmmod.o
     1991    gfortran: erreur interne du compilateur: le signal Erreur du bus a
              terminé le programme f951
     1992    Veuillez soumettre un rapport d’anomalies complet,
     1993    avec la sortie du préprocesseur si nécessaire.
     1994    Voir <https://gcc.gnu.org/bugs/> pour les instructions.
     1995    gmakefile:164: recipe for target 'arch-linux2-c-opt/obj/dm/f90-mod
             /petscdmmod.o' failed
  >> 1996    make[2]: *** [arch-linux2-c-opt/obj/dm/f90-mod/petscdmmod.o] Error
              4
     1997    make[2]: Leaving directory '/tmp/B87457/spack-stage/spack-stage-_f
             hph4/petsc-3.9.3'
     1998    /tmp/B87457/spack-stage/spack-stage-_fhph4/petsc-3.9.3/lib/petsc/c
             onf/rules:81: recipe for target 'gnumake' failed
  >> 1999    make[1]: *** [gnumake] Error 2
     2000    make[1]: Leaving directory '/tmp/B87457/spack-stage/spack-stage-_f
             hph4/petsc-3.9.3'
     2001    **************************ERROR***********************************
             **
     2002      Error during compile, check arch-linux2-c-opt/lib/petsc/conf/mak
             e.log
     2003      Send it and arch-linux2-c-opt/lib/petsc/conf/configure.log to pe
             tsc-...@mcs.anl.gov
     2004    ******************************************************************
             **
     2005    makefile:30: recipe for target 'all' failed
  >> 2006    make: *** [all] Error 1

Is that mean that I should launch:

"""

spack install -j 4 mofem-users-modules%g...@8.2.0 ?

"""

Regards

[Dzifa Kudawoo]

I just try:

"""

spack install mofem-users-modules%g...@8.2.0, It seems to fix the problem.

"""

Regards

[Dzifa Kudawoo]

Update:

I've got this error when installing mofem-cephas:

"""

==> Error: ProcessError: Command exited with status 2:

    'make' '-j8'

"""

I try then this command:

"""

spack install -j 4 mofem-users-modules%g...@8.2.0, It seems to fix the problem.

"""

Result of the installation:

==> Installing mofem-users-modules
==> Fetching file:///home/B87457/mofem/install_dir/spack-mirror-2018-11-05/mofem-users-modules/mofem-users-modules-0.8.15.tar.gz
######################################################################## 100,0%
==> Warning: Fetching from mirror without a checksum!
  This package is normally checked out from a version control system, but it has been archived on a spack mirror.  This means we cannot know a checksum for the tarball in advance. Be sure that your connection to this mirror is secure!
==> Staging archive: /gpfseole/home/B87457/mofem/install_dir/spack/var/spack/stage/mofem-users-modules-0.8.15-sbvuyvhn3j4hemao66sgvbtxvki3uore/mofem-users-modules-0.8.15.tar.gz
==> Created stage in /gpfseole/home/B87457/mofem/install_dir/spack/var/spack/stage/mofem-users-modules-0.8.15-sbvuyvhn3j4hemao66sgvbtxvki3uore
==> No patches needed for mofem-users-modules
==> Building mofem-users-modules [CMakePackage]
==> Executing phase: 'cmake'
==> Executing phase: 'build'
==> Executing phase: 'install'
==> Successfully installed mofem-users-modules
  Fetch: 0.12s.  Build: 3m 13.41s.  Total: 3m 13.53s.
[+] /gpfseole/home/B87457/mofem/install_dir/spack/opt/spack/linux-debian8-x86_64/gcc-8.2.0/mofem-users-modules-0.8.15-sbvuyvhn3j4hemao66sgvbtxvki3uore

I can finally launch a simple elasticity test:

"""

mpirun -np 2 ./elasticity -my_file LShape.h5m -ksp_type gmres -pc_type lu -pc_factor_mat_solver_package mumps -ksp_monitor -my_order 2

"""

I try to launch a thermal_unsteady test, but I've got an error:

"""

mpirun -np 2 ./thermal_steady   -my_file simple_thermal_problem.cub    -ksp_type fgmres -pc_type lu -pc_factor_mat_solver_package mumps -ksp_monitor   -my_order 4 -my_max_post_proc_ref_level 2

"""

[0]MOAB ERROR: --------------------- Error Message ------------------------------------
[0]MOAB ERROR: simple_thermal_problem.cub: No such file or directory!

Question:

Where can I find in the test database this kind of file ?

[Lukasz Kaczmraczyk]

Hello,

It looks that you have successfully install code, well done. 

For thermal problem you missing mesh file, you can get it from here:

https://bitbucket.org/likask/mofem-cephas/src/master/mofem/meshes/

Now you can install mofem fracture module, 

spack install -j 4 mofem-fracture-module

Regards,

Lukasz

[Dzifa Kudawoo]

Thanks Lukasz:

Update for the installation of fracture mechanics.

I try

"""

spack install -j 4 mofem-fracture-module

"""

I've got this error:

"""

==> Installing mofem-fracture-module
==> Fetching file:///home/B87457/mofem/install_dir/spack-mirror-2018-11-05/mofem-fracture-module/mofem-fracture-module-0.9.48.tar.gz
curl: (37) Couldn't open file /home/B87457/mofem/install_dir/spack-mirror-2018-11-05/mofem-fracture-module/mofem-fracture-module-0.9.48.tar.gz
==> Fetching from file:///home/B87457/mofem/install_dir/spack-mirror-2018-11-05/mofem-fracture-module/mofem-fracture-module-0.9.48.tar.gz failed.
==> Cloning git repository: https://bitbucket.org/likask/mofem_um_fracture_mechanics at tag v0.9.48
fatal: unable to access 'https://bitbucket.org/likask/mofem_um_fracture_mechanics/': Failed to connect to bitbucket.org port 443: Connection refused
fatal: unable to access 'https://bitbucket.org/likask/mofem_um_fracture_mechanics/': Failed to connect to bitbucket.org port 443: Connection refused
==> Fetching from [git] https://bitbucket.org/likask/mofem_um_fracture_mechanics failed.
==> Error: FetchError: All fetchers failed for mofem-fracture-module-0.9.48-s2lv6g5upvgf7raicylbbeedrdgemaay

/gpfseole/home/B87457/mofem/install_dir/spack/lib/spack/spack/package.py:934, in do_fetch:

        931                raise FetchError("Will not fetch %s" %
        932                                 self.spec.format('$_$@'), ck_msg)
        933
  >>    934        self.stage.create()
        935        self.stage.fetch(mirror_only)
        936        self._fetch_time = time.time() - start_time

        937
"""

Then I realize that in my mirror, in the directory I do not have spack-mirror-2018-11-05/mofem-fracture-module/

The output of:

"""

ls -l  spack-mirror-2018-11-05/mofem-fracture-module/

"""

is

"""

total 0

"""

When trying to add it in my local machine:

"""

spack mirror create -D mofem-fracture-module

"""

I have this error.

"""

==> Successfully updated mirror in spack-mirror-2018-11-06
  Archive stats:
    39   already present
    0    added

    1    failed to fetch.
==> Error: Failed downloads:

"""

Any advice?

May be, I could download by hand but I worry that it is the way to do that.

[Dzifa Kudawoo]

The error of fetching mofem-fracture-mechanics is:

"""

==> Adding package mofem-frac...@0.9.48 to mirror

==> Cloning git repository: https://bitbucket.org/likask/mofem_um_fracture_mechanics at tag v0.9.48

warning: Could not find remote branch v0.9.48 to clone.
fatal: Remote branch v0.9.48 not found in upstream origin
warning: Could not find remote branch v0.9.48 to clone.
fatal: Remote branch v0.9.48 not found in upstream origin
==> Warning: Error while fetching mofem-frac...@0.9.48
  Command exited with status 128:
==

"""

[Dzifa Kudawoo]

Now I have copied the mofem-fracture-mechanics on the local mirror and then launc the install command with "-j  4" but I have a problem building mofem-fracture-mecanics:

"""
==> Executing phase: 'cmake'
==> Executing phase: 'build'

==> Error: ProcessError: Command exited with status 2:

    'make' '-j4'

"""

I'm not sure but may be some option of compilation may be passed to avoid this? CCFLAGS=XXXX ?

[Dzifa Kudawoo]

Just as a reminder, I install the compiler, curl, ...etc by passing -j 8 as argument and building mofem-users-module with -j 4 options.

May be there is incompatibility between this two option of compilation. If so, how can I clean properly the compilation option -j 8 and reinstall again gcc ?

[Lukasz Kaczmraczyk]

Hello,

I apologise about that, I forget to push tag to version v0.9.48. Now that is fixed. You can pull module to mirror.

Kind regards,

Lukasz

[Dzifa Kudawoo]

Hi Lukasz,

I got the same error:

"""

==> Installing mofem-fracture-module
==> Fetching file:///home/B87457/mofem/install_dir/spack-mirror-2018-11-05/mofem-fracture-module/mofem-fracture-module-0.9.48.tar.gz

######################################################################## 100,0%
==> Warning: Fetching from mirror without a checksum!
  This package is normally checked out from a version control system, but it has been archived on a spack mirror.  This means we cannot know a checksum for the tarball in advance. Be sure that your connection to this mirror is secure!

==> Staging archive: /gpfseole/home/B87457/mofem/install_dir/spack/var/spack/stage/mofem-fracture-module-0.9.48-s2lv6g5upvgf7raicylbbeedrdgemaay/mofem-fracture-module-0.9.48.tar.gz
==> Created stage in /gpfseole/home/B87457/mofem/install_dir/spack/var/spack/stage/mofem-fracture-module-0.9.48-s2lv6g5upvgf7raicylbbeedrdgemaay
==> No patches needed for mofem-fracture-module
==> Building mofem-fracture-module [CMakePackage]

==> Executing phase: 'cmake'
==> Executing phase: 'build'

==> Error: ProcessError: Command exited with status 2:

    'make' '-j4'

4 errors found in build log:
     3029       ^~~~~~~~~~~~~~~~~~
     3030    g++: erreur interne du compilateur: le signal Erreur du bus a terminé le programme cc1plus
     3031    Veuillez soumettre un rapport d’anomalies complet,
     3032    avec la sortie du préprocesseur si nécessaire.
     3033    Voir <https://gcc.gnu.org/bugs/> pour les instructions.
     3034    mofem_um_fracture_mechanics/CMakeFiles/fm_crack_propagation.dir/build.make:78: recipe for target 'mof
             em_um_fracture_mechanics/CMakeFiles/fm_crack_propagation.dir/src/impl/CPSolvers.cpp.o' failed
  >> 3035    make[2]: *** [mofem_um_fracture_mechanics/CMakeFiles/fm_crack_propagation.dir/src/impl/CPSolvers.cpp.
             o] Error 4

"""

[Lukasz Kaczmraczyk]

Can you try

spack install -j 1 mofem-users-modules%g...@8.2.0

This problems with crashing compiler could be because low memory on head node.

[Dzifa Kudawoo]

GOOD NEWS guys! It seems to be installed. I just need to make a quick test to be sure that everything is good.

How can I test the fracture module using tests that are already installed ?

 

==> Installing mofem-fracture-module

==> Fetching file:///home/B87457/mofem/install_dir/spack-mirror-2018-11-05/mofem-fracture-module/mofem-fracture-module-0.9.48.tar.gz
######################################################################## 100,0%
==> Warning: Fetching from mirror without a checksum!
  This package is normally checked out from a version control system, but it has been archived on a spack mirror.  This means we cannot know a checksum for the tarball in advance. Be sure that your connection to this mirror is secure!
==> Staging archive: /gpfseole/home/B87457/mofem/install_dir/spack/var/spack/stage/mofem-fracture-module-0.9.48-s2lv6g5upvgf7raicylbbeedrdgemaay/mofem-fracture-module-0.9.48.tar.gz
==> Created stage in /gpfseole/home/B87457/mofem/install_dir/spack/var/spack/stage/mofem-fracture-module-0.9.48-s2lv6g5upvgf7raicylbbeedrdgemaay
==> No patches needed for mofem-fracture-module
==> Building mofem-fracture-module [CMakePackage]
==> Executing phase: 'cmake'
==> Executing phase: 'build'

==> Executing phase: 'install'
==> Successfully installed mofem-fracture-module
  Fetch: 0.18s.  Build: 6m 21.94s.  Total: 6m 22.11s.
[+] /gpfseole/home/B87457/mofem/install_dir/spack/opt/spack/linux-debian8-x86_64/gcc-8.2.0/mofem-fracture-module-0.9.48-s2lv6g5upvgf7raicylbbeedrdgemaay

[Lukasz Kaczmraczyk]

You can create vie to fracture module:

spack view --verbose symlink -i fracture_v0.9.48_view mofem-frac...@0.9.48

Then you can run code from directory 

fracture_v0.9.48_view/mofem_um_fracture_mechanicsEnter

In future you could make updares of mofem, and you will be able to keep sunsequent versions of mofem 

[Dzifa Kudawoo]

GREAT NEWS! I can say it WORKS fine:

Test under mofem-fracture-mechanics directory:

"""

 mpirun -np 4 ./crack_propagation -my_file examples/sslp114/sslp114.h5m  -my_order 2 -mofem_mg_verbose 1 -mofem_mg_coarse_order 1 -mofem_mg_levels 2 -my_ref 1 -my_geom_order 1 -my_ref_order 1 -material HOOKE -nb_load_steps 1 -load_scale 1  2>&1 | tee log0

"""

This issue ticket could be closed.

Many THANKS to Lukasz and Karol.