Merge pull request #19 from PawseySC/pelahi-readme-update

Added some readme's to containers that need special launch states

mpi/lustrempich-base/README.md

@@ -0,0 +1,52 @@
+# Lustre+MPI
+
+This container provides a basis for running parallel io on HPE Cray EX systems. It does this by providing a
+lustre-aware mpi. Then by mounting the appropriate libraries (mpich and associated dependencies, lustre and associated depds) 
+into the container, the container will be able to run parallel IO such as parallel HDF5 or ADIOS2.
+
+For completeness, here we provide how the lmod module would add various paths for binding the libraries into the host
+
+```lua
+
+-- example for a lmod module where we set the singularity environments to these 
+local singularity_ld_path = "/opt/cray/pe/mpich/default/ofi/gnu/9.1/lib-abi-mpich:/opt/cray/pe/mpich/default/gtl/lib:/opt/cray/xpmem/default/lib64:/opt/cray/pe/pmi/default/lib:/opt/cray/pe/pals/default/lib"
+singularity_ld_path = singularity_ld_path .. ":/opt/cray/pe/gcc-libs"
+singularity_ld_path = singularity_ld_path .. ":/opt/cray/libfabric/1.15.2.0/lib64/"
+
+-- BIND_PATH addition
+local singularity_bindpath = "/some_standard_paths"
+-- add CRAY_PATHS START
+singularity_bindpath = singularity_bindpath .. ",/var/opt/cray/pe,/etc/opt/cray/pe,/opt/cray,/etc/alternatives/cray-dvs,/etc/alternatives/cray-xpmem"
+-- singularity_bindpath = singularity_bindpath .. ",/lib64/libc.so.6,/lib64/libpthread.so.0,/lib64/librt.so.1,/lib64/libdl.so.2,/lib64/libz.so.1,/lib64/libselinux.so.1,/lib64/libm.so.6"
+-- add MPI START
+singularity_bindpath = singularity_bindpath .. ",/usr/lib64/libcxi.so.1,/usr/lib64/libcurl.so.4,/usr/lib64/libjson-c.so.3"
+singularity_bindpath = singularity_bindpath .. ",/usr/lib64/libnghttp2.so.14,/usr/lib64/libidn2.so.0,/usr/lib64/libssh.so.4,/usr/lib64/libpsl.so.5,/usr/lib64/libssl.so.1.1,/usr/lib64/libcrypto.so.1.1,/usr/lib64/libgssapi_krb5.so.2,/usr/lib64/libldap_r-2.4.so.2,/usr/lib64/liblber-2.4.so.2,/usr/lib64/libunistring.so.2,/usr/lib64/libkrb5.so.3,/usr/lib64/libk5crypto.so.3,/lib64/libcom_err.so.2,/usr/lib64/libkrb5support.so.0,/lib64/libresolv.so.2,/usr/lib64/libsasl2.so.3,/usr/lib64/libkeyutils.so.1,/usr/lib64/libpcre.so.1"
+-- new additions for libfabric 1.15.2.0
+singularity_bindpath = singularity_bindpath .. ",/usr/lib64/libjitterentropy.so.3,/usr/lib64/libbrotlidec.so.1,/usr/lib64/libbrotlicommon.so.1,/usr/lib64/libjansson.so.4"
+singularity_bindpath = singularity_bindpath .. ",/usr/lib64/libzstd.so.1"
+singularity_bindpath = singularity_bindpath .. ",/lib64/libselinux.so.1"
+-- lustre 
+singularity_bindpath = singularity_bindpath .. ",/usr/lib64/liblustreapi.so.1,/usr/lib64/liblnetconfig.so.4,/usr/lib64/libyaml-0.so.2,/usr/lib64/libnl-genl-3.so.200,/usr/lib64/libnl-3.so.200"
+
+-- LD_PRELOAD addition 
+local singularity_ld_preload = ""
+-- add MPI START
+-- preload xpmem for fast mpi communication
+singularity_ld_preload = singularity_ld_preload .. ":/opt/cray/xpmem/default/lib64/libxpmem.so.0"
+-- singularity_ld_preload = singularity_ld_preload .. ":/lib64/libc.so.6:/lib64/libpthread.so.0:/lib64/librt.so.1:/lib64/libdl.so.2:/lib64/libz.so.1:/lib64/libselinux.so.1:/lib64/libm.so.6"
+-- for Cassini nics and SS>=11
+singularity_ld_preload = singularity_ld_preload .. ":/usr/lib64/libcxi.so.1:/usr/lib64/libcurl.so.4:/usr/lib64/libjson-c.so.3"
+singularity_ld_preload = singularity_ld_preload .. ":/usr/lib64/libnghttp2.so.14:/usr/lib64/libidn2.so.0:/usr/lib64/libssh.so.4:/usr/lib64/libpsl.so.5:/usr/lib64/libssl.so.1.1:/usr/lib64/libcrypto.so.1.1:/usr/lib64/libgssapi_krb5.so.2:/usr/lib64/libldap_r-2.4.so.2:/usr/lib64/liblber-2.4.so.2:/usr/lib64/libunistring.so.2:/usr/lib64/libkrb5.so.3:/usr/lib64/libk5crypto.so.3:/lib64/libcom_err.so.2:/usr/lib64/libkrb5support.so.0:/lib64/libresolv.so.2:/usr/lib64/libsasl2.so.3:/usr/lib64/libkeyutils.so.1:/usr/lib64/libpcre.so.1"
+-- authentication 
+singularity_ld_preload = singularity_ld_preload .. ":/usr/lib64/libmunge.so.2"
+-- new additions for libfabric 1.15.2.0
+singularity_ld_preload = singularity_ld_preload .. ":/usr/lib64/libjitterentropy.so.3:/usr/lib64/libbrotlidec.so.1:/usr/lib64/libbrotlicommon.so.1:/usr/lib64/libjansson.so.4"
+singularity_ld_preload = singularity_ld_preload .. ":/usr/lib64/liblustreapi.so.1:/usr/lib64/liblnetconfig.so.4:/usr/lib64/libyaml-0.so.2:/usr/lib64/libnl-genl-3.so.200:/usr/lib64/libnl-3.so.200"
+singularity_ld_preload = singularity_ld_preload .. ":/usr/lib64/libzstd.so.1"
+singularity_ld_preload = singularity_ld_preload .. ":/lib64/libselinux.so.1"
+-- lustre
+singularity_ld_preload = singularity_ld_preload .. ":/usr/lib64/liblustreapi.so.1:/usr/lib64/liblnetconfig.so.4:/usr/lib64/libyaml-0.so.2:/usr/lib64/libnl-genl-3.so.200:/usr/lib64/libnl-3.so.200"
+-- add MPI END
+```
+
+

slurm/README.md

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+# How to use this container
+
+This container provides slurm inside a container so jobs can be launched from a container. It does this by providing slurm 
+in a container (that needs to match that outside). Then by mounting the appropriate paths for authentication and configuration
+slurm can be run from inside the container and behave like slurm on the host. 
+
+For completeness, here we provide how the lmod module would add various paths for binding the libraries into the host
+
+```lua
+-- Singularity configuration START
+-- LD_LIBRARY_PATH addition
+local singularity_ld_path = ""
+setenv("SINGULARITYENV_LD_LIBRARY_PATH", singularity_ld_path)
+
+-- add SLURM START
+singularity_bindpath = singularity_bindpath .. ",/var/run/munge/munge.socket.2,/etc/slurm"
+-- add SLURM END
+
+setenv("SINGULARITY_BINDPATH",singularity_bindpath)
+```