Installing Cardinal on an offline HPC Cluster

[nancysemwal]

I am trying to install Cardinal on an offline HPC Cluster. Since there is no separate article listing the offline installation instructions, I'm following the same Building Cardinal without MOOSE's conda Environment steps and also referring to offline MOOSE installation.

The error I'm encountering occurs in ./contrib/moose/scripts/update_and_rebuild_libmesh.sh step

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-- Done configuring core library features ---
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----- Configuring for optional packages -----
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checking for built-in XDR support... no
checking for XDR support in /usr/include/tirpc... no
configure: error: *** XDR was not found, but --enable-xdr-required was specified.
Running make -j 32...
make: *** No targets specified and no makefile found.  Stop.

After looking at some discussions here, I tried to solve this by setting --disable-xdr in contrib/moose/scripts/configure_libmesh.sh and it compiled. However make -j8 failed with this output

Linking Executable /home/user/cardinal/cardinal-opt...
/home/user/cardinal/contrib/moose/modules/stochastic_tools/lib/libstochastic_tools-opt.so: undefined reference to `void libMesh::Parallel::Packing<std::tuple<unsigned int, unsigned int, std::shared_ptr<libMesh::DenseVector<double> > >, void>::pack<std::back_insert_iterator<std::vector<double, std::allocator<double> > >, void>(std::tuple<unsigned int, unsigned int, std::shared_ptr<libMesh::DenseVector<double> > > const&, std::back_insert_iterator<std::vector<double, std::allocator<double> > >, void const*)'
/home/user/cardinal/contrib/moose/modules/stochastic_tools/lib/libstochastic_tools-opt.so: undefined reference to `libMesh::Parallel::Packing<std::tuple<unsigned int, unsigned int, std::shared_ptr<libMesh::DenseVector<double> > >, void>::packed_size(__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >)'
/home/user/cardinal/contrib/moose/modules/stochastic_tools/lib/libstochastic_tools-opt.so: undefined reference to `std::tuple<unsigned int, unsigned int, std::shared_ptr<libMesh::DenseVector<double> > > libMesh::Parallel::Packing<std::tuple<unsigned int, unsigned int, std::shared_ptr<libMesh::DenseVector<double> > >, void>::unpack<__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, void>(__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, void*)'
/home/user/cardinal/contrib/moose/modules/stochastic_tools/lib/libstochastic_tools-opt.so: undefined reference to `libMesh::Parallel::Packing<std::tuple<unsigned int, unsigned int, std::shared_ptr<libMesh::DenseVector<double> > >, void>::packable_size(std::tuple<unsigned int, unsigned int, std::shared_ptr<libMesh::DenseVector<double> > > const&, void const*)'
collect2: error: ld returned 1 exit status
make: *** [/home/user/cardinal/contrib/moose/framework/[app.mk:466](http://app.mk:466/): /home/user/cardinal/cardinal-opt] Error 1

I have encountered a similar issue involving another .so file which I had solved by using an older commit of the devel branch instead of using git clone https://github.com/neams-th-coe/cardinal.git, the very first installation step. This had worked last time when I was installing it on my PC but not working this time.

How do I proceed from here?

[nuclearkevin]

Hi @nancysemwal,

It looks like contrib/moose/modules/stochastic_tools/src/util/VectorPacker.C isn't getting compiled for some reason (possibly due to a header-source mismatch). I don't know how to resolve this one, so my recommendation (at the moment) is to disable the stochastic tools module if you don't need it (and it's the only linker error). You can do this by going to Cardinal's Makefile and setting STOCHASTIC_TOOLS := no. I'll do some more digging to see if there are other fixes, but this should get you up and running for the moment.

Hope that helps,
Kevin

[rishabh10gpt]

Can we enforce the compilation of VectorPacker.C file? and can you please guide about which make file is compiling stochastic_tools?

[aprilnovak]

Each MOOSE module (stochastic_tools included) is compiled into Cardinal by first calling cardinal/contrib/moose/modules/modules.mk (you can find this file referenced in Cardinal's Makefile.