GEOS-5

Building CVS Baselibs

Revision as of 06:32, 8 February 2013 by Mathomp4 (talk | contribs) (→Intel 11)

This page will detail the process of building Baselibs. For the purposes of this page, GMAO-Baselibs-4_0_1 as an example tag, but this process should work with any "recent" tag (say, GMAO-Baselibs-3_3_0 or higher).

Check out Baselibs

The first step is to check out the tag you want.

Set up the 'bcvs' alias

Something useful to set up first is an alias that you can use to refer to the CVS repo for Baselibs. This is because the Baselibs are hosted on progress while the GEOS-5 model and most other tools are on the CVSACL repo. So, I recommend setting a 'bcvs' alias: 

$ alias bcvs 'cvs -d:ext:USERNAME@progressdirect:/cvsroot/baselibs'

where USERNAME is your username at progress. Note that this works on discover and pleiades, but elsewhere you'll need to set up a tunnel to progress and alter the CVSROOT appropriately.

Checking out the tag

Next, checkout the tag: 

$ bcvs co -r GMAO-Baselibs-4_0_1 -d GMAO-Baselibs-4_0_1 Baselibs

This will create a GMAO-Baselibs-4_0_1 inside which is a src directory.

Build Baselibs

The next task is to build Baselibs. In order to correctly build it, two arguments are needed: ESMF_COMM and CONFIG_SETUP. ESMF_COMM is the MPI stack used by ESMF (usually, mvapich2, mpi, openmpi, or intelmpi). CONFIG_SETUP is actually an "identifier" that will allow you to build multiple versions of Baselibs for multiple compiler/MPI combination. The style recommended is for, say, Intel 13.0.1.117 and MVAPICH2 1.9a2 is: CONFIG_SETUP=ifort_13.0.1.117-mvapich2_1.9a2 where you identify the compiler (by its name on the command line), its version, the MPI stack, and its version.

So for the above example you'd issue: 

$ make install ESMF_COMM=mvapich2 CONFIG_SETUP=ifort_13.0.1.117-mvapich2_1.9a2 |& tee makeinstall.ifort_13.0.1.117-mvapich2_1.9a2.log

and it would build all the libraries. The tee is so that you can capture the install log, and also see it real-time. Note that the modules installed for above (say on discover) are: 

1) comp/intel-13.0.1.117
2) other/mpi/mvapich2-1.9a2/intel-13.0.1.117
3) other/comp/gcc-4.6.3-sp1
4) other/SIVO-PyD/spd_1.6.0_gcc-4.6.3-sp1

or run: 

$ module purge
$ module load comp/intel-13.0.1.117 other/mpi/mvapich2-1.9a2/intel-13.0.1.117 other/comp/gcc-4.6.3-sp1 other/SIVO-PyD/spd_1.6.0_gcc-4.6.3-sp1

Once built, check for "Error" in your log file: 

$ grep Error makeinstall.ifort_13.0.1.117-mvapich2_1.9a2.log
	    (test $HDF5_Make_Ignore && echo "*** Error ignored") ||          \
	    (test $HDF5_Make_Ignore && echo "*** Error ignored") ||          \
      H5Eset_auto2(H5E_DEFAULT, PrintErrorStackFunc, PrintErrorStackData);
make[6]: [install-exec-hook] Error 1 (ignored)
make[6]: [install-data-hook] Error 1 (ignored)
      Whimper ( "Error creating scratch file" ) ;
/usr/local/other/SLES11.1/mvapich2/1.9a2/intel-13.0.1.117/bin/mpicc  -c -O2 -DH5_USE_16_API -DLINUX64 -Df2cFortran -DHDF4_NETCDF_HAVE_SD -DLINUX64 -DPGS_MET_COMPILE   -I/discover/swdev/mathomp4/Baselibs/GMAO-Baselibs-4_0_1/src/SDPToolkit/include -I/discover/swdev/mathomp4/Baselibs/GMAO-Baselibs-4_0_1/src/SDPToolkit/include/CUC -I/discover/swdev/mathomp4/Baselibs/GMAO-Baselibs-4_0_1/x86_64-unknown-linux-gnu/ifort_13.0.1.117-mvapich2_1.9a2/Linux/include/hdf -I/discover/swdev/mathomp4/Baselibs/GMAO-Baselibs-4_0_1/x86_64-unknown-linux-gnu/ifort_13.0.1.117-mvapich2_1.9a2/Linux/include/hdf5 PGS_MET_ErrorMsg.c -o /discover/swdev/mathomp4/Baselibs/GMAO-Baselibs-4_0_1/src/SDPToolkit/obj/linux64/MET/PGS_MET_ErrorMsg.o
cp PGS_MET_ErrorMsg.o tmp/METErrorMsg.o

If you don't see any "Error 2" messages, you are probably safe.


Checking Baselibs

This is optional, but recommended. Many of the Baselibs have the ability to do a check. You should do this only in an environment where you can run MPI (like compute nodes at NCCS or NAS). This is because parallel NetCDF and ESMF tests are run: 

$ make check ESMF_COMM=mvapich2 CONFIG_SETUP=ifort_13.0.1.117-mvapich2_1.9a2 |& tee makecheck.ifort_13.0.1.117-mvapich2_1.9a2.log

Note that at the moment, many will exit with errors. For example, NetCDF has tests that require internet access.

Modules

Discover

Intel 11

comp/intel-11.0.083 mpi/impi-3.2.2.006 lib/mkl-10.0.3.020 other/SIVO-PyD/spd_1.6.0_gcc-4.3.4-sp1

Intel 13

comp/intel-13.0.1.117 other/mpi/mvapich2-1.9a2/intel-13.0.1.117 other/comp/gcc-4.6.3-sp1 other/SIVO-PyD/spd_1.6.0_gcc-4.6.3-sp1
comp/intel-13.0.1.117 mpi/impi-4.0.3.008 other/comp/gcc-4.6.3-sp1 other/SIVO-PyD/spd_1.6.0_gcc-4.6.3-sp1
comp/intel-13.0.1.117 mpi/impi-4.0.1.007-beta other/comp/gcc-4.6.3-sp1 other/SIVO-PyD/spd_1.6.0_gcc-4.6.3-sp1

PGI 12

comp/pgi-12.8.0 other/mpi/openmpi/1.6.0-pgi-12.8.0 other/comp/gcc-4.6.3-sp1 other/SIVO-PyD/spd_1.6.0_gcc-4.6.3-sp1
comp/pgi-12.8.0 other/mpi/mvapich2-1.8/pgi-12.8.0 other/comp/gcc-4.6.3-sp1 other/SIVO-PyD/spd_1.6.0_gcc-4.6.3-sp1

Pleiades

Intel 11

comp/intel/11.0.083_64 mpi-intel/3.2.011 math/intel_mkl_64_10.0.011 python/2.6.1
comp/intel/11.0.083_64 mpi-sgi/mpt.2.06a67 math/intel_mkl_64_10.0.011 python/2.6.1

Intel 12

comp-intel/2012.0.032 mpi-sgi/mpt.2.06a67 python/2.6.1

PGI 12

pgi_12.8 mvapich2_1.8.1_pgi_12.8 python/2.6.1
pgi_12.8 mpi-sgi/mpt.2.06a67 python/2.6.1
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