Building CVS Baselibs

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.

Load modules

For our example we want to load these modules:

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

For other modules see the table at the end.

Note: It's a good idea to build Baselibs in a clean environment. If you have cruft in, say, LD_LIBRARY_PATH, it's possible the build will not pick up the libraries you expect.

Undo any CPP Environment Variable

Before doing any make, you should issue:

$ unsetenv CPP DEFAULT_CPP

Some modules set these and most of the Baselibs assume the C-preprocessor will be gcc, not, say, pgcpp.

Set MPICC_CC and MPICXX_CXX variables if using MPT

If you are using MPT at Pleiades, you must set the MPICC_CC and MPICXX_CXX variables to be the "correct" compilers. This can be done either in the environment full (beware!) or during the install by adding at the end:

MPICC_CC=icc  MPICXX_CXX=icpc
MPICC_CC=pgcc MPICXX_CXX=pgCC

Build and install

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.

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.

Checking with Intel MPI

Note that if you use Intel MPI as the MPI stack, when you run the check (on discover) you have to manually run mpdboot to start a mpd ring:

$ mpdboot -n 8 -r ssh -f $PBS_NODEFILE

This example is for 8 nodes.

Table of Modules

Discover
Compiler	MPI Stack	Other Libraries
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
	mpi/impi-4.0.3.008
	other/mpi/mvapich2-1.8.1/intel-11.0.083
	other/mpi/openmpi/1.6.0-intel-11.0.083
comp/intel-13.0.1.117	other/mpi/mvapich2-1.8.1/intel-13.0.1.117	other/comp/gcc-4.6.3-sp1 other/SIVO-PyD/spd_1.6.0_gcc-4.6.3-sp1
	mpi/impi-4.0.3.008
comp/intel-13.1.0.146	other/mpi/mvapich2-1.8.1/intel-13.1.0.146
	mpi/impi-4.0.3.008
	other/mpi/openmpi/1.6.3-intel-13.1.0.146
comp/pgi-12.8.0	other/mpi/openmpi/1.6.3-pgi-12.8.0
	other/mpi/mvapich2-1.8/pgi-12.8.0
Pleiades
Compiler	MPI Stack	Other Libraries
comp/intel/11.0.083_64	mpi-intel/3.2.011	math/intel_mkl_64_10.0.011 python/2.6.1
	mpi-sgi/mpt.2.06a67
	mpi-sgi/mpt.2.06rp16
comp-intel/2012.0.032	mpi-sgi/mpt.2.06a67	python/2.6.1
comp-intel/2013.1.117	mpi-sgi/mpt.2.06rp16
	mpi-intel/4.0.2.003
pgi_12.8	mvapich2_1.8.1_pgi_12.8
	mpi-sgi/mpt.2.06a67
	mpi-sgi/mpt.2.06rp16