From 6937fc86d58f0e102217825ba3fb53a31ba738a4 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 4 Jul 2024 12:00:13 +0200
Subject: [PATCH] fix CI: change base image from CentOS7 to Ubuntu 22.04
---
.gitlab-ci.yml | 98 ++++++++++++++++++--------------------------------
1 file changed, 34 insertions(+), 64 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c24946cd1..6476bce78 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,76 +6,45 @@
stages:
- test
-# CentOS7 STAGE
-test:centos7.3:
+# Ubuntu22.04 STAGE
+test:ubuntu22.04:
stage: test
- image: centos:7.3.1611
+ image: ubuntu:22.04
before_script:
- - echo "Running centos7.3 'before_script'..."
- - yum -y -q -e 0 install tcl
- - yum -y -q -e 0 install glibc-common
- - yum -y -q -e 0 install glibc-devel
- - yum -y -q -e 0 install make
- - yum -y -q -e 0 install libicu
- - yum -y -q -e 0 install libjpeg-turbo
- - yum -y -q -e 0 install freetype
- - yum -y -q -e 0 install openssl
- - mkdir -p /scicore/soft/modules
- - ln -s /export/soft/apps/centos7/generic /scicore/soft/apps
- - ln -s /export/soft/modules/centos7/generic/all /scicore/soft/modules
- - source /export/soft/lua_lmod/centos7/lmod/lmod/init/bash
- - module use /scicore/soft/modules/all
- - module load foss/2021a
- - module load wget/1.21.1-GCCcore-10.3.0
- - module load CMake/3.23.1-GCCcore-10.3.0
- - module load Python/3.9.5-GCCcore-10.3.0
- - module load Eigen/3.4.0-GCCcore-10.3.0
- - module load Boost.Python/1.76.0-GCC-10.3.0
- - module load LibTIFF/.4.2.0-GCCcore-10.3.0
- - module load libpng/.1.6.37-GCCcore-10.3.0
- - module load HH-suite/3.2.0-gompi-2021a
- - module load Perl/5.32.1-GCCcore-10.3.0
- - module load OpenMM/7.7.0-foss-2021a
- - module load SQLite/3.35.4-GCCcore-10.3.0
- - module load dssp/2.2.1-foss-2021a
- - module load msms/2.6.1-linux-x86_64
- - module load ClustalW2/2.1-foss-2021a
- - module load networkx/2.5.1-foss-2021a
- - echo "... done running centos7.3 'before_script'."
+ - echo "Running ubuntu22.04 'before_script'..."
+ - apt-get update -y
+ - apt-get install -y cmake
+ - apt-get install -y g++
+ - apt-get install -y wget
+ - apt-get install -y libsqlite3-dev
+ - apt-get install -y sip-dev
+ - apt-get install -y libtiff-dev
+ - apt-get install -y libfftw3-dev
+ - apt-get install -y libeigen3-dev
+ - apt-get install -y libboost-all-dev
+ - apt-get install -y libpng-dev
+ - apt-get install -y python3-all
+ - apt-get install -y python3-numpy
+ - apt-get install -y python3-scipy
+ - apt-get install -y python3-networkx
+ - apt-get install -y clustalw
+ - apt-get install -y voronota
+ - apt-get install -y libopenmm-dev
+ - apt-get install -y libparasail-dev
+ - echo "... done running ubuntu22.04 'before_script'."
script:
- - echo "Testing on CentOS 7..."
+ - echo "Testing on Ubuntu 22.04..."
- echo " Building OST..."
- mkdir build-ci
- cd build-ci
- - cmake .. -DENABLE_MM=1
- -DOPEN_MM_LIBRARY=$EBROOTOPENMM/lib/libOpenMM.so
- -DOPEN_MM_PLUGIN_DIR=$EBROOTOPENMM/lib/plugins
- -DOPEN_MM_INCLUDE_DIR=$EBROOTOPENMM/include
- -DCOMPILE_TMTOOLS=1
- -DENABLE_INFO=OFF
- -DENABLE_GFX=OFF
+ - cmake .. -DOPTIMIZE=ON
+ -DENABLE_GFX=ON
-DENABLE_GUI=OFF
- -DUSE_RPATH=1
- -DPython_ROOT_DIR=$EBROOTPYTHON
- -DEIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include
- -DFFTW_LIBRARY=$EBROOTFFTW/lib/libfftw3f.a
- -DFFTW_INCLUDE_DIR=$EBROOTFFTW/include
- -DSQLITE3_LIBRARY=$EBROOTSQLITE/lib/libsqlite3.so
- -DSQLITE3_INCLUDE_DIR=$EBROOTSQLITE/include
- -DBOOST_ROOT=$EBROOTBOOST
- -DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so
- -DPNG_PNG_INCLUDE_DIR=$EBROOTLIBPNG/include
- -DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so
- -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include
- -DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include
- -DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.so
- -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include
- -DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so
- -DOPTIMIZE=1
- -DCMAKE_C_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
- -DCMAKE_CXX_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
- -DCMAKE_EXE_LINKER_FLAGS=" -pthread"
- - make -j 2 chemdict_tool
+ -DENABLE_INFO=OFF
+ -DENABLE_MM=1
+ -DOPEN_MM_PLUGIN_DIR=/usr/lib/x86_64-linux-gnu/openmm
+ -DENABLE_PARASAIL=1
+ - make -j 2
- echo " ... done building OST."
- echo " Downloading chemical compounds..."
- wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
@@ -91,4 +60,5 @@ test:centos7.3:
- echo " Running unit tests for OST..."
- make check
- echo " ... done running unit tests for OST..."
- - echo "... done testing on CentOS 7."
+ - echo "... done testing on Ubuntu 22.04."
+
--
GitLab