Bad alloc error

[Emmanuel-324]

Check these boxes if you have followed the posting rules.

• Q&A General is the most appropriate section for my question
• I have consulted the posting Guidelines on the Discussions front page
• I have searched the Discussions forum and my question has not been asked before
• I have searched the MOOSE website and the documentation does not answer my question
• I have formatted my post following the posting guidelines (screenshots as a last resort, triple back quotes around pasted text)

Question

I get this error output , any help

std::bad_alloc

[GiudGiud]

Hello

Please follow the debugging instructions and get us a backtrace. That will show where the problem

Guillaume

[Emmanuel-324]

I did it again and below is the error I run into

(python-stack) [emmanuel324@tinkercliffs1 belson]$ METHOD=dbg make -j 8
Linking Library /home/emmanuel324/projects/moose/framework/contrib/pcre/libpcre-dbg.la...
Linking Library /home/emmanuel324/projects/moose/framework/contrib/hit/libhit-dbg.la...
Linking Executable /home/emmanuel324/projects/moose/framework/contrib/exodiff/exodiff...
Linking Library /home/emmanuel324/projects/moose/modules/chemical_reactions/lib/libchemical_reactions-dbg.la...
Linking Library /home/emmanuel324/projects/moose/modules/electromagnetics/lib/libelectromagnetics-dbg.la...
Linking Library /home/emmanuel324/projects/moose/modules/external_petsc_solver/lib/libexternal_petsc_solver-dbg.la...
Linking Library /home/emmanuel324/projects/moose/modules/fluid_properties/lib/libfluid_properties-dbg.la...
Linking Library /home/emmanuel324/projects/moose/modules/functional_expansion_tools/lib/libfunctional_expansion_tools-dbg.la...
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: cannot find -lmesh_dbg: No such file or directory
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: cannot find -ltimpi_dbg: No such file or directory
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: cannot find -lmesh_dbg: No such file or directory
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: cannot find -ltimpi_dbg: No such file or directory
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: cannot find -lmesh_dbg: No such file or directory
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: cannot find -ltimpi_dbg: No such file or directory
Linking Library /home/emmanuel324/projects/moose/modules/geochemistry/lib/libgeochemistry-dbg.la...
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libutil.so when searching for -lutil
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libutil.so when searching for -lutil
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libutil.so when searching for -lutil
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread
/apps/easybuild/software/tinkercliffs-rome/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread
collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status
make: *** [/home/emmanuel324/projects/moose/framework/contrib/pcre/libpcre-dbg.la] Error 1
make: *** Waiting for unfinished jobs....
collect2: error: ld returned 1 exit status
make: *** [/home/emmanuel324/projects/moose/framework/contrib/exodiff/exodiff] Error 1
make: *** [/home/emmanuel324/projects/moose/framework/contrib/hit/libhit-dbg.la] Error 1

[milljm]

when you see missing libMesh libraries like this:

 -lmesh_dbg: No such file or directory

It means libMesh needs to be built in the same method you are trying to build your application. In your case dbg.
Or, if you have already built libMesh in this method, your application can't find it (perhaps LIBMESH_DIR is not set).

Re-reading your earlier posts, something must have gone wrong with:

cd ~/projects/moose/scripts
export MOOSE_JOBS=6 METHODS="opt dbg"
./update_and_rebuild_petsc.sh
./update_and_rebuild_libmesh.sh      <----- something happened
./update_and_rebuild_wasp.sh

FYI, you don't need to do the following when changing methods:

./update_and_rebuild_petsc.sh
./update_and_rebuild_wasp.sh

[Emmanuel-324]

All that I did before my initial post was follow the initial procedure of MOOSE installation which comes without the "dbg". When I do:

cd ~/projects/moose/scripts
export MOOSE_JOBS=6 METHODS="opt dbg"
./update_and_rebuild_libmesh.sh    

Would I have to create a new application following the instructions on the MOOSE page?

[milljm]

Shouldn't have to... I don't think one would even need to clean their repo when building multiple methods. I am basically saying, if you were happily running with an opt version, and then needed to build a dbg version... METHOD=dbg make is really all that is necessary... so long as libMesh was also built with that method.

When running ./update_and_rebuild_libmesh.sh without any arguments, libMesh should build the following methods: opt dbg devel oprof.

In your case, it should have built opt dbg. But something went wrong if we're running into missing libraries.

Can you run the following, and report the configure.log / any errors etc?

cd ~/projects/moose/scripts
export MOOSE_JOBS=6 METHODS="opt dbg"
./update_and_rebuild_libmesh.sh

[Emmanuel-324]

Got this error at the end @milljm

 CXX      src/utils/libmesh_dbg_la-plt_loader_read.lo
../src/utils/perf_log.C: In member function 'std::string libMesh::PerfLog::get_info_header() const':
../src/utils/perf_log.C:268:42: error: 'LIBMESH_CONFIGURE_INFO' was not declared in this scope
  268 |       std::string libmesh_configure_info(LIBMESH_CONFIGURE_INFO);
      |                                          ^~~~~~~~~~~~~~~~~~~~~~
make[1]: *** [src/utils/libmesh_dbg_la-perf_log.lo] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory `/home/emmanuel324/projects/moose/libmesh/build'
make: *** [all-recursive] Error 1