Amanzi build error

[Kewei Chen]

Hi all,

I am trying to install ATS on my own machine and HPC in school. Everything was good on my Ubuntu machine, but building Amanzi failed on HPC (see attached screenshort). I don't know if it's because I didn't install lapack on HPC due to limited permission. Any suggestions are appreciated.

Best,

Kewei

[Ethan Coon]

The problem seems to be in linking with boost.  I'm guessing that either bootstrap's TPL build was unable to build boost (which means you should have seen an earlier issue and it wouldn't have gotten this far) or maybe more likely, the build is getting confused by a system boost installation (we've had lots of trouble with system boosts before).

Can you cd into your AMANZI_BUILD_DIR, run:

$> VERBOSE=1 make &> make.log

then send the resulting make.log file?  Can you also check -- is there a /usr/lib/libboost* or a /usr/local/lib/libboost* on your system?

Ethan

[Lipnikov, Konstantin]

Boost has issues with correct installation of shared libraries. Try to add the location of Boost libraries to the standard (for your system) environmental variable, LIBRARY_PATH or similar. 

Konstantin

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To: Amanzi-ATS Users
Subject: [EXTERNAL] Re: Amanzi build error

 

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[Coon, Ethan]

Oh, great point.  To expand upon what Konstantin is saying, likely for an HPC machine (assuming Linux based), you’ll want to make sure you have:

 

export LD_LIBRARY_PATH=${AMANZI_TPLS_DIR}:${LD_LIBRARY_PATH}

 

in your setup/bashrc/however you are managing your environment variables.  You may find you need to add Trilinos paths to that too, e.g.

 

export LD_LIBRARY_PATH=${AMANZI_TPLS_DIR}/trilinos-VERSION-NUMBER:${AMANZI_TPLS_DIR}:${LD_LIBRARY_PATH}

 

and similar for other things that cannot be found on linking.

 

Ethan

 

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Oak Ridge National Laboratory

 

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[David Moulton]

Hi Guys,

  

     Just to confirm my experience looking at this lately, I agree with Konstantin and Ethan here ( hope to have this fixed for real sometime soon).  If you set the LD_LIBRARY_PATH as Ethan suggests it should work.  Note the error in linking was for a test, and the library is likely built and installed as expected.  So adding to LD_LIBRARY_PATH should do the trick.  

If it doesn't you could add it to LIBRARY_PATH as well.  The reported difference is that LIBRARY_PATH is used during build and link, and LD_LIBRARY_PATH is used at runtime (but I'm not sure this distinction is really observed in practice).

Cheers, David

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[Kewei Chen]

Thanks for all your suggestions! ATS has been successfully compiled on HPC. One more issue is an error message shows up when I submit the job to cluster:

ASCEMIO_Info: Preferred group size is set to nprocs/numIOgroups (1/1) 

ASCEMIO_Info: Preferred group size is set to 1 

ASCEMIO_Info: Preferred group size is set to nprocs/numIOgroups (1/1) 

ASCEMIO_Info: Preferred group size is set to 1 

[r13n45:428486] *** An error occurred in MPI_Comm_create_keyval

[r13n45:428486] *** reported by process [1879572481,140733193388032]

[r13n45:428486] *** on communicator MPI_COMM_WORLD

[r13n45:428486] *** MPI_ERR_ARG: invalid argument of some other kind

[r13n45:428486] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,

[r13n45:428486] ***    and potentially your MPI job)

It seems like mpi is not working on HPC. 

For my ubuntu machine, ATS can run, but warning messages keep showing:

HDF5-DIAG: Error detected in HDF5 (1.10.6) MPI-process 0:

  #000: /home/kchen/ats/amanzi_tpls-build-master-Debug/hdf5/hdf5-1.10.6-source/src/H5S.c line 490 in H5Sclose(): not a dataspace

    major: Invalid arguments to routine

    minor: Inappropriate type

I am not sure which one, hdf5 or mpi, cause the issue.

Thanks,

Kewei