From c72e0ca558b9a0859cdf98ed0d331fd86f8c2114 Mon Sep 17 00:00:00 2001
From: "Mulas, Giacomo" <gmulas@oa-cagliari.inaf.it>
Date: Fri, 10 May 2024 14:29:15 +0200
Subject: [PATCH] - update pipeline runner config - fix logger race in omp
threads - add mpi to docker images
---
.gitlab-ci.yml | 2 ++
containers/docker/Dockerfile | 4 +++-
src/cluster/cluster.cpp | 13 ++++++++-----
3 files changed, 13 insertions(+), 6 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1290ed98..7e740501 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -63,6 +63,8 @@ compatibility_stage:
- make clean && PATH=/opt/intel/oneapi/compiler/latest/bin:$PATH BUILDDIR=$PWD/../build_ifort-icpx CXX=icpx FC=ifort FCFLAGS="-O3 -diag-disable=10448" make -j
- echo "Running make with Intel ifx and Intel icpx..."
- make clean && LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/latest/lib PATH=/opt/intel/oneapi/compiler/latest/bin:$PATH BUILDDIR=$PWD/../build_ifx-icpx CXX=icpx FC=ifx FCFLAGS=-O3 make -j
+ - echo "Running make with default MPI compilers"
+ - make clean && BUILDDIR=$PWD/../build_mpi CXX=mpicxx FC=mpif90 USE_MPI=1 make -j
building_stage:
stage: build
diff --git a/containers/docker/Dockerfile b/containers/docker/Dockerfile
index 2f528d22..0b456148 100644
--- a/containers/docker/Dockerfile
+++ b/containers/docker/Dockerfile
@@ -20,6 +20,8 @@ RUN apt update
RUN DEBIAN_FRONTEND=noninteractive apt -y install intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-compiler-dpcpp-cpp
# install lapacke and its dependencies, both standard and the version with 64 bit integers
RUN DEBIAN_FRONTEND=noninteractive apt -y install liblapacke-dev liblapacke64-dev libopenblas-dev libopenblas-openmp-dev libopenblas64-dev libopenblas64-openmp-dev
+# install MPI stack
+RUN DEBIAN_FRONTEND=noninteractive apt -y install mpi-default-dev mpi-default-bin
# install packages needed to run python scripts for checks
RUN DEBIAN_FRONTEND=noninteractive apt -y install python3 python-is-python3 python3-regex
# install packages needed to run doxygen to create html docs
@@ -53,7 +55,7 @@ FROM debian:bookworm-slim AS np-tmcode-run-minimal
WORKDIR /root
# install the strictly needed runtime libraries needed to run the executables
# and the python check scripts
-RUN DEBIAN_FRONTEND=noninteractive apt update && DEBIAN_FRONTEND=noninteractive apt upgrade && DEBIAN_FRONTEND=noninteractive apt -y install libgfortran5 libgcc-s1 libhdf5-103-1 libstdc++6 libssl3 libcurl4 libsz2 zlib1g libnghttp2-14 libidn2-0 librtmp1 libssh2-1 libpsl5 libgssapi-krb5-2 libldap-2.5-0 libzstd1 libbrotli1 libaec0 libunistring2 libgmp10 libkrb5-3 libk5crypto3 libcom-err2 libkrb5support0 libsasl2-2 libp11-kit0 libtasn1-6 libkeyutils1 libffi8 liblapacke64 libopenblas64-0-openmp python3 python-is-python3 python3-regex hdf5-tools && rm -rf /var/lib/apt/lists/*
+RUN DEBIAN_FRONTEND=noninteractive apt update && DEBIAN_FRONTEND=noninteractive apt upgrade && DEBIAN_FRONTEND=noninteractive apt -y install libgfortran5 libgcc-s1 libhdf5-103-1 libstdc++6 libssl3 libcurl4 libsz2 zlib1g libnghttp2-14 libidn2-0 librtmp1 libssh2-1 libpsl5 libgssapi-krb5-2 libldap-2.5-0 libzstd1 libbrotli1 libaec0 libunistring2 libgmp10 libkrb5-3 libk5crypto3 libcom-err2 libkrb5support0 libsasl2-2 libp11-kit0 libtasn1-6 libkeyutils1 libffi8 liblapacke64 libopenblas64-0-openmp python3 python-is-python3 python3-regex hdf5-tools mpi-default-bin && rm -rf /var/lib/apt/lists/*
COPY --from=np-tmcode-run-dev /root /root
# remove everything which is not needed to run the codes
RUN cd /root/np-tmcode && find build -name "*.o" -exec rm -v \{\} \; && find build -name "*.gcno" -exec rm -v \{\} \; && cd src && rm -rvf cluster libnptm trapping include sphere Makefile make.inc README.md && cd .. && rm -rvf containers && cd doc && rm -rvf src && cd build/latex && rm -rvf *.tex *.out *.sty *.ind *.log *.toc *.ilg *.idx *.aux *.eps Makefile class*.pdf
diff --git a/src/cluster/cluster.cpp b/src/cluster/cluster.cpp
index 306dafa3..6bb1272c 100644
--- a/src/cluster/cluster.cpp
+++ b/src/cluster/cluster.cpp
@@ -58,7 +58,7 @@ using namespace std;
// I would like to put it all in a struct, but then I'd have to write a constructor for it, due to members defined as references, creating a worse nightmare than the one I'd like to simplify...
-int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConfiguration *gconf, ScatteringAngles *sa, ClusterIterationData *cid, FILE *output, const string& output_path, fstream& tppoan, Logger *logger);
+int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConfiguration *gconf, ScatteringAngles *sa, ClusterIterationData *cid, FILE *output, const string& output_path, fstream& tppoan);
/*! \brief C++ implementation of CLU
*
@@ -183,7 +183,7 @@ void cluster(const string& config_file, const string& data_file, const string& o
// do the first iteration on jxi488 separately, since it seems to be different from the others
int jxi488 = 1;
chrono::time_point<chrono::high_resolution_clock> start_iter_1 = chrono::high_resolution_clock::now();
- int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid, output, output_path, tppoan, logger);
+ int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid, output, output_path, tppoan);
chrono::time_point<chrono::high_resolution_clock> end_iter_1 = chrono::high_resolution_clock::now();
elapsed = start_iter_1 - t_start;
message = "INFO: Calculation setup took " + to_string(elapsed.count()) + "s.\n";
@@ -238,7 +238,7 @@ void cluster(const string& config_file, const string& data_file, const string& o
// ok, now I can actually start the parallel calculations
#pragma omp for
for (jxi488 = cid_2->firstxi; jxi488 <= cid_2->lastxi; jxi488++) {
- int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid_2, output_2, output_path, *tppoanp_2, logger);
+ int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid_2, output_2, output_path, *tppoanp_2);
}
#pragma omp barrier
@@ -396,7 +396,7 @@ void cluster(const string& config_file, const string& data_file, const string& o
// ok, now I can actually start the parallel calculations
#pragma omp for
for (int jxi488 = cid_2->firstxi; jxi488 <= cid_2->lastxi; jxi488++) {
- int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid_2, output_2, output_path, *tppoanp_2, logger);
+ int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid_2, output_2, output_path, *tppoanp_2);
}
#pragma omp barrier
@@ -466,10 +466,11 @@ void cluster(const string& config_file, const string& data_file, const string& o
delete logger;
}
-int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConfiguration *gconf, ScatteringAngles *sa, ClusterIterationData *cid, FILE *output, const string& output_path, fstream& tppoan, Logger *logger)
+int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConfiguration *gconf, ScatteringAngles *sa, ClusterIterationData *cid, FILE *output, const string& output_path, fstream& tppoan)
{
int nxi = sconf->number_of_scales;
string message = "INFO: running scale iteration " + to_string(jxi488) + " of " + to_string(nxi) + ".\n";
+ Logger *logger = new Logger(LOG_INFO);
logger->log(message);
chrono::duration<double> elapsed;
chrono::time_point<chrono::high_resolution_clock> interval_start, interval_end;
@@ -1128,5 +1129,7 @@ int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConf
logger->log("INFO: finished scale iteration " + to_string(jxi488) + " of " + to_string(nxi) + ".\n");
+ delete logger;
+
return jer;
}
--
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