Install Request: LAMMPS 15th June 2023 release but doing 2nd August 2023 [IN06098486]

[balston]

The 15th June 2023 release includes for the first time support to output vector style variables during a simulation run which this research group needs.

It looks like the latest version in Spack is 8 Feb 2023.

https://www.lammps.org/download.html

[heatherkellyucl]

Ticket now IN:06149543.

[balston]

LAMMPS 2nd August 2023 is now the latest release so install this one.

[balston]

A build of LAMMPS 2nd August 2023 using GNU compilers and FFTW is now on Myriad and Young using our build scripts method:

module -f unload compilers mpi gcc-libs
module load beta-modules
./lammps-2Aug2023-basic-fftw-gnu_install 2>&1 | tee ~/Software/LAMMPS/lammps-2Aug2023-basic-fftw-gnu_install.log-1

Need to produce a module file and run some tests next.

[balston]

I now have the module file on Myriad and Young and have submitted test jobs on both clusters.

[balston]

Both the test jobs on Myriad and Young worked. Modules needed for basic GNU FFTW version are:

Myriad

module -f unload compilers mpi gcc-libs
module load beta-modules
module load gcc-libs/10.2.0
module load compilers/gnu/10.2.0
module load numactl/2.0.12
module load binutils/2.36.1/gnu-10.2.0
module load ucx/1.9.0/gnu-10.2.0
module load mpi/openmpi/4.0.5/gnu-10.2.0
module load python3/3.9-gnu-10.2.0
module load fftw/3.3.9/gnu-10.2.0
module load lammps/2aug23/basic-fftw/gnu-10.2.0 

Young

module -f unload compilers mpi gcc-libs
module load beta-modules
module load gcc-libs/10.2.0
module load compilers/gnu/10.2.0
module load mpi/openmpi/4.0.5/gnu-10.2.0
module load python3/3.9-gnu-10.2.0
module load fftw/3.3.9/gnu-10.2.0
module load lammps/2aug23/basic-fftw/gnu-10.2.0

[balston]

Now working on the GNU + GPU build.

Build script updated and pulled to Young. Needs to be built on a GPU node so job submitted to build LAMMPS 2nd August 2023 GNU+GPU on Young. Build script:

lammps-2Aug2023-gpu-gnu_install

[balston]

Build job for LAMMPS 2nd August 2023 GNU+GPU submitted on Myriad as well.

[balston]

Both jobs are running.

[balston]

CPU build done on Kathleen and test job submitted.

[balston]

I've only had time today to check the output from the test job on Kathleen. It looks like it has worked ok.

[balston]

Look at:

/home/ccspapp/Software/LAMMPS/tmp.2P0AWpwdjR/lammps-2Aug2023/cmake/presets/most.cmake

for list of LAMMPS packages in our default CPU builds.

[balston]

I had to redo the GPU builds on Myriad and Young as I had missed out the FFTW module.

The Myriad build has completed and a job running the GPU unit tests has been submitted.

Young build job is still waiting.

[balston]

Test jobs for the GPU build have been submitted on Myriad and Young.

[balston]

I've also been trying a build of the basic Intel version but this is failing during compilation:

/dev/shm/ccspapp/lammps/tmp.v9Hhxi8WAq/lammps-stable_2Aug2023/build/_deps/googletest-src/googletest/include/gtest/gtest-matchers.h(434): error: namespace "std" has no member "is_trivially_copy_constructible"
             std::is_trivially_copy_constructible<M>::value &&
                  ^
          detected during:
            processing of template argument list for "testing::internal::MatcherBase<T>::ValuePolicy [with T=const std::string &]" based on template argument <MM> at line 483
            instantiation of "void testing::internal::MatcherBase<T>::Init(M &&) [with T=const std::string &, M=const testing::MatcherInterface<const std::string &> *&]" at line 312
            instantiation of "testing::internal::MatcherBase<T>::MatcherBase(const testing::MatcherInterface<U> *) [with T=const std::string &, U=const std::string &]" at line 536

/dev/shm/ccspapp/lammps/tmp.v9Hhxi8WAq/lammps-stable_2Aug2023/build/_deps/googletest-src/googletest/include/gtest/gtest-matchers.h(434): error: type name is not allowed
             std::is_trivially_copy_constructible<M>::value &&
                                                  ^
          detected during:
            processing of template argument list for "testing::internal::MatcherBase<T>::ValuePolicy [with T=const std::string &]" based on template argument <MM> at line 483
            instantiation of "void testing::internal::MatcherBase<T>::Init(M &&) [with T=const std::string &, M=const testing::MatcherInterface<const std::string &> *&]" at line 312
            instantiation of "testing::internal::MatcherBase<T>::MatcherBase(const testing::MatcherInterface<U> *) [with T=const std::string &, U=const std::string &]" at line 536

/dev/shm/ccspapp/lammps/tmp.v9Hhxi8WAq/lammps-stable_2Aug2023/build/_deps/googletest-src/googletest/include/gtest/gtest-matchers.h(434): error: the global scope has no "value"
             std::is_trivially_copy_constructible<M>::value &&
                                                      ^
          detected during:
            processing of template argument list for "testing::internal::MatcherBase<T>::ValuePolicy [with T=const std::string &]" based on template argument <MM> at line 483
            instantiation of "void testing::internal::MatcherBase<T>::Init(M &&) [with T=const std::string &, M=const testing::MatcherInterface<const std::string &> *&]" at line 312
            instantiation of "testing::internal::MatcherBase<T>::MatcherBase(const testing::MatcherInterface<U> *) [with T=const std::string &, U=const std::string &]" at line 536

compilation aborted for /dev/shm/ccspapp/lammps/tmp.v9Hhxi8WAq/lammps-stable_2Aug2023/build/_deps/googletest-src/googletest/src/gtest-all.cc (code 2)
make[2]: *** [_deps/googletest-build/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o] Error 2
make[2]: Leaving directory `/dev/shm/ccspapp/lammps/tmp.v9Hhxi8WAq/lammps-stable_2Aug2023/build'
make[1]: *** [_deps/googletest-build/googletest/CMakeFiles/gtest.dir/all] Error 2
make[1]: Leaving directory `/dev/shm/ccspapp/lammps/tmp.v9Hhxi8WAq/lammps-stable_2Aug2023/build'
make: *** [all] Error 2

Using Intel 2020 compilers.

[heatherkellyucl]

I would use compilers/intel/2022.2 and not 2020 for anything (because of newer gcc underneath).

[balston]

Updated Intel build to use gcc-libs/10.2.0 and Intel 2022.2:

module -f unload compilers mpi gcc-libs
module load beta-modules
BUILD_UNIT_TESTS=yes ./lammps-2Aug2023-basic_install 2>&1 | tee ~/Software/LAMMPS/lammps-2Aug2023-basic_install.log-2

[balston]

The test jobs for the GNU + GPU version have run successfully on Myriad and Young.

[balston]

The basic Intel build on Myriad completed without errors using Intel 2022.2 compilers. It will need testing now.

[balston]

I've submitted a test job for the basic Intel version on Myriad.

[balston]

The LAMMPS 2nd August 2023 basic Intel version test job runs on Myriad. I'm now going to build this version on Kathleen and Young.

[balston]

The builds on Kathleen and Young have finished. Will now need to check for errors and run a 2 node or bigger test job.

[balston]

Two node test job for the basic Intel version submitted on Kathleen.

[balston]

Two node test job for the basic Intel version submitted on Young.

[balston]

The Kathleen job has been running for 6 hours (set for about 12). The Young one is still queueing.

[balston]

Both jobs finished overnight and look ok. The Kathleen one was a bigger job and did 20,000 in about 8 hours and the smaller Young one 2000 steps in 48 minutes. I'll upload a module file for the basic Intel version.

[balston]

module file updated and loaded onto Kathleen, Myriad and Young.

[balston]

To use LAMMPS 2nd August 2023 version basic Intel build you need the following modules:

module -f unload compilers mpi gcc-libs
module load beta-modules
module load gcc-libs/10.2.0
module load compilers/intel/2022.2
module load mpi/intel/2019/update6/intel
module load python/3.9.10
module load lammps/2aug23/basic/intel-2022.2

[balston]

Doing the build with the INTEL package next. On Kathleen first:

module -f unload compilers mpi gcc-libs
module load beta-modules
./lammps-2Aug2023-INTEL_install 2>&1 | tee ~/Software/LAMMPS/lammps-2Aug2023-INTEL_instal.log

[balston]

The INTEL build on Kathleen has completed without errors.

[balston]

I have a test job submitted for the INTEL build on Kathleen.