Building CVS Baselibs: Difference between revisions
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This page will detail the process of building Baselibs. For the purposes of this page, GMAO-Baselibs- | This page will detail the process of building Baselibs. For the purposes of this page, GMAO-Baselibs-4_0_7 as an example tag, but this process should work with any recent tag. | ||
==Check out Baselibs== | ==Check out Baselibs== | ||
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Next, checkout the tag: | Next, checkout the tag: | ||
$ bcvs co -r GMAO-Baselibs- | $ bcvs co -r GMAO-Baselibs-4_0_7 -d GMAO-Baselibs-4_0_7 Baselibs | ||
This will create a <tt>GMAO-Baselibs- | This will create a <tt>GMAO-Baselibs-4_0_7</tt> inside which is a <tt>src</tt> directory. | ||
== Build Baselibs == | == Build Baselibs == | ||
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For our example we want to load these modules: | For our example we want to load these modules: | ||
1) comp/intel-15.0.2.164 | |||
2) mpi/impi-5.0.3.048 | |||
3) lib/mkl-15.0.2.164 | |||
4) other/comp/gcc-4.6.3-sp1 | |||
5) other/SIVO-PyD/spd_1.20.0_gcc-4.6.3-sp1_mkl-15.0.0.090 | |||
For other modules see the table at the end. | For other modules see the table at the end. | ||
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=== Undo any CPP Environment Variable === | === Undo any CPP Environment Variable === | ||
Before doing any make, you should issue: | Before doing any make (especially with PGI), you should issue: | ||
$ unsetenv CPP DEFAULT_CPP | $ unsetenv CPP DEFAULT_CPP | ||
Some modules set these and most of the Baselibs assume the C-preprocessor will be gcc, not, say, pgcpp. | Some modules set these and most of the Baselibs assume the C-preprocessor will be gcc, not, say, pgcpp (which is '''not''' a C++ compiler!). | ||
=== Set MPICC_CC and MPICXX_CXX variables if using MPT === | === (OPTIONAL) 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: | If you are using MPT at Pleiades, and you wish to use the Intel or PGI C and C++ compilers instead of GNU, 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=icc MPICXX_CXX=icpc | ||
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So for the above example you'd issue: | So for the above example you'd issue: | ||
$ make install ESMF_COMM= | $ make install ESMF_COMM=intelmpi CONFIG_SETUP=ifort_15.0.2.164-intelmpi_5.0.3.048 |& tee makeinstall.ifort_15.0.2.164-intelmpi_5.0.3.048.log | ||
and it would build all the libraries. The <tt>tee</tt> is so that you can capture the install log, and also see it real-time. | and it would build all the libraries. The <tt>tee</tt> is so that you can capture the install log, and also see it real-time. | ||
Once built, check for "Error" in your log file | Once built, check for "Error" in your log file, and if you don't see any "<tt>Error 2</tt>" messages, you are probably safe. | ||
==== make verify ==== | |||
make | |||
You can also use <tt>make verify</tt> which will check the status of the build (by looking for xxx.config and xxx.install files) and print a table like: | |||
-------+---------+---------+-------------- | |||
Config | Install | Check | Package | |||
-------+---------+---------+-------------- | |||
ok | ok | -- | jpeg | |||
ok | ok | -- | zlib | |||
ok | ok | -- | szlib | |||
ok | ok | -- | curl | |||
ok | ok | -- | hdf4 | |||
ok | ok | -- | hdf5 | |||
ok | ok | -- | h5edit | |||
ok | ok | -- | netcdf | |||
ok | ok | -- | netcdf-fortran | |||
ok | ok | -- | udunits2 | |||
ok | ok | -- | nco | |||
ok | ok | -- | cdo | |||
ok | ok | -- | esmf | |||
ok | ok | -- | hdfeos | |||
ok | ok | -- | uuid | |||
ok | ok | -- | cmor | |||
ok | ok | -- | hdfeos5 | |||
ok | ok | -- | SDPToolkit | |||
-------+---------+---------+-------------- | |||
Note that this is not as comprehensive as looking at the log file as it is possible that some submakes will fail but not communicate that well enough to the main make process. | |||
== Checking Baselibs == | == Checking Baselibs == | ||
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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: | 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= | $ make check ESMF_COMM=intelmpi CONFIG_SETUP=ifort_15.0.2.164-intelmpi_5.0.3.048 |& tee makecheck.ifort_15.0.2.164-intelmpi_5.0.3.048.log | ||
Note that at the moment, many will exit with errors. For example, NetCDF has tests that require internet access. | Note that at the moment, many will exit with errors. For example, NetCDF has tests that require internet access and if a check is done on a compute node with no external access, it will fail. | ||
=== Checking with Intel MPI === | === 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 <tt>mpdboot</tt> to start a mpd ring: | Note that if you use an older Intel MPI as the MPI stack, when you run the check (on discover) you may have to manually run <tt>mpdboot</tt> to start a mpd ring: | ||
$ mpdboot -n 8 -r ssh -f $PBS_NODEFILE | $ mpdboot -n 8 -r ssh -f $PBS_NODEFILE | ||
This example is for 8 nodes. | This example is for 8 nodes. This is not because of Intel MPI ''per se'' but because of codes like netcdf-C that use <tt>mpiexec</tt> as its call to start an MPI process. In Intel MPI older than 2017, mpiexec calls the old MPD version and not Hydra. | ||
== Table of Modules == | == Table of Modules == | ||