Chef/Building
This goes over how to compile Chef and some system specific instructions for doing so.
Contents
General Instruction
For students looking to see what compiled successfully on the viz nodes, please go to /users/mabl7046/Group_Dir. The workflow is exactly the same as what is outlined below, however, the scripts were of course altered to set the environment properly for the viz nodes.
Note that .smdmodels made with a new version of simModeler will likely only work with chef compiled with a recent version of simModSuite.
Common Errors
The following error is very common when Compiling Chef: CMake Error at cmake/FindSimModSuite.cmake:93 (MESSAGE):
invalid Simmetrix version: 15.0.201010, valid versions are 12.0.190225 to 15.0.200714. When this is encountered, the SCORE/core source code must be changed. From the build directory vim the file FindSimModSuite.cmake. This is in the directory /core/cmake. Scroll down to line 87 and edit set(MAX_VALID_SIM_VERSION 15.0.200714) to a Simmetrix version within the range of the version you are using to compile.
System Specific
Summit (RMACC)
Copy Simmetrix Libraries from Viz Nodes
Note that in order for Chef to operate, it must be compiled with the proper Simmetrix libraries. That is to say, there needs to be compatibility between Simmetrix and SCOREC-core for compilation of Chef to run smoothly. Please see Building SCOREC Core for instructions on cloning the source code. An example (what worked for me) is provided throughout the wiki. From the viz nodes (/projects/tools/SimmetrixTest), I ran
scp -r 14.0-190626beta/ <username>@login.rc.colorado.edu:<path>
to copy over the directory 14.0-190626beta/ to Summit.
Set Proper Environment
To start with a clean slate, run
module purge
This unloads all currently loaded modules.
Next, run
module load gcc/6.1.0 module load openmpi/2.0.1
Note that /6.1.0 and /2.0.1 can be swapped with the intended versions of GCC and OpenMPI the user intends on using.
Generate Partition Wrapper
After the directory is copied over to Summit and the environment is set, a Partition Wrapper needs to be generated. Go to:
<path>/14.0-190626beta/code/PartitionWrapper
and open the file
Makefile.custom
Obviously, 14.0-190626beta/ is a placeholder and any version of Simmetrix (i.e. the version you used to create the mesh) will work. In this example, I used OpenMPI . I also used mpicc and mpicxx as MPI-C and MPI-C++ compilers respectively. If this is what is intended, in the Makefile, set the following variables:
PQUAL:= -openmpi CC:=/curc/sw/openmpi/2.0.1/gcc/6.1.0/bin/mpicc CXX:= /curc/sw/openmpi/2.0.1/gcc/6.1.0/bin/mpicxx
Notice the compatibility between the loaded modules and the directory structure above. Once this is set, in the terminal run
make -f Makefile.custom PARALLEL=openmpi
This will generate a file named libSimPartitionWrapper-openmpi.a. Then, run
chmod +x libSimPartitionWrapper-openmpi.a.
Once this is completed, copy this newly generated partition wrapper to ../../lib/x64_rhel7_gcc48/. Unfortunately, the instructions from this point forward will be less explicit as the best way to learn the process is to view example scripts and adapt these to fit your needs. From this point forward, it is assumed that a directory named SCOREC-core was created and the source code from GitHub was properly cloned in this directory.
Generating the Scripts to Compile Chef
In order to run Chef, two scripts must be generated. The naming conventions of the scripts are typically doConfigure.sh and env_simmtrix_version. Below, an example doConfigure.sh script is shown. This script primarily executes the necessary CMake commands for compilation. It also runs the env_simmtrix_version script. In the example below, it calls env_14.0-190626. Note that both of these scripts are located in /projects/mabl7046/SCOREC-core/build_14.0-190626, or the directory where Chef is to be compiled. Note that the line -DMESHES="/projects/mabl7046/pumi-meshes" was copied from a script that implemented successfully on another machine. I recommend looking at scripts on the Viz nodes that worked for the version of Chef you are compiling and copying over the directory analogous to pumi-meshes to summit to implement your script.
doConfigure.sh:
#!/bin/bash -l . /projects/mabl7046/SCOREC-core/build_14.0-190626/env_14.0-190626 #unload default modules module purge #load what we need module load gcc/6.1.0 module load openmpi/2.0.1 module load cmake/3.14.1 ### For Chef cmake -DCMAKE_C_COMPILER=mpicc \ -DCMAKE_CXX_COMPILER=mpicxx \ -DSCOREC_CXX_WARNINGS=ON \ -DSCOREC_CXX_OPTIMIZE=ON \ -DSCOREC_CXX_SYMBOLS=ON \ -DPCU_COMPRESS=ON \ -DENABLE_ZOLTAN=ON \ -DENABLE_SIMMETRIX=ON \ -DSIM_MPI="openmpi" \ -DSIM_PARASOLID=ON \ -DMDS_SET_MAX=1024 \ -DMDS_ID_TYPE=long \ -DIS_TESTING=OFF \ -DMESHES="/projects/mabl7046/pumi-meshes" \ -DCMAKE_INSTALL_PREFIX=$PWD/install \ ../core #-DMDS_ID_TYPE=int or long sleep 3 make -j32 make -j32
Below, the script env_14.0-190626 is given. As stated in the comments, this is to set the environment for CMake.SCOREC. In order to make this script work, the SIM_LICENSE_FILE (denoted UCBoulder below) needed to be obtained. The libraries for Zoltan and parmetis also needed to be collected. The SIM_LICENSE_FILE was copied over from Cooley although, I am sure that this can be obtained from the Viz nodes as well. To obtain the libraries for Zoltan and parmetis on Summit, run:
cp -r /projects/ASEN5119/SCOREC-core/deps/zoltan . cp -r /projects/ASEN5119/SCOREC-core/deps/parmetis .
from the directory where you wish these to be. All this does is move these from a directory Ken created for his Boundary Layers course to a directory that is more convenient for personal use.
env_14.0-190626:
### For CMake.SCOREC export buildRoot=/projects/mabl7046/SCOREC-core/ export simModVer=$buildRoot/deps/Simmetrix/14.0-190626beta/ export SIM_LICENSE_FILE=$buildRoot/deps/Simmetrix/UCBoulder export CMAKE_PREFIX_PATH=$simModVer export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$simModVer/lib/x64_rhel7_gcc48 export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$simModVer/lib/x64_rhel7_gcc48/psKrnl #MIGHT NEED THIS export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:/projects/tools/Simmetrix.develop/simModSuite/PartitionWrapper/lib ### For Zoltan and parmetis export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$buildRoot/deps/zoltan/3.83-gnu49-ompi210/ export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$buildRoot/deps/parmetis/4.0.3-gnu492-ompi210 # the following is to give the path to PartitionWrappers that have not been installed in the Simmetrix library export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$simModVer/code/PartitionWrapper/lib
Final Notes
Once the scripts are set up, simply run ./doConfigure.sh to compile the code. Please be patient with the process as it is highly unlikely that it will compile successfully the first time you try. Be sure to pay close attention to your directory structure when setting your scripts up and be cognizant of the dependencies between programs.
