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Commit 6e4eb098 authored by Antoine Cyril David Hoffmann's avatar Antoine Cyril David Hoffmann :seedling:
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update auto installer for spcpc

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scripts/tutorials/spcpc_installation_auto.sh
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#! /bin/bash
# This tutorial helps you install Gyacomo on an SPC medusa PC, based on OpenSUSE and intel compiler. You will be guided from the cloning of the repository to the first run.
# Record the start time
start=$(date +%s)
# Display title
echo '=============================================='
echo ' ______ '
echo ' / ____/_ ______ __________ ____ ___ ____ '
......@@ -13,12 +17,12 @@ echo '=============================================='
# 1. Prelude
# 1.1 - First, we clone the repository.
echo -- 1. Clone the directory
git clone https://gitlab.epfl.ch/ahoffman/gyacomo.git > gyacomo_clone.out
echo "1. Clone the directory "
git clone https://gitlab.epfl.ch/ahoffman/gyacomo.git &> gyacomo_clone.out
cd gyacomo
# 1.2 - Then we purge and load the following modules (the default one may be of older intel compiler version, which will not work with FFTW3).
echo -- Purge and load the modules
echo " Purge and load the modules"
module purge
module load intel_comp/19.1 impi/5.0.3 mumps/4.10.0 hdf5/1.8.9
......@@ -26,7 +30,7 @@ module load intel_comp/19.1 impi/5.0.3 mumps/4.10.0 hdf5/1.8.9
# cd gyacomo
# 1.4 - Finally, we make a `lib` directory (here we make it in `/gyacomo` but it can be anywhere as long as the path to it is set correctly in `gyacomo/local/dirs.inc`).
echo -- make lib directory
echo " make lib directory"
mkdir lib
# **Important:** Verify that the `gyacomo/local/dirs.inc` file points to your `gyacomo` folder in the `PREFIX` variable and to your `lib` folder in the `LIBDIR` variable.
......@@ -39,11 +43,16 @@ mkdir lib
# - FFTW3, the Fastest Fourier Transform in the West version 3, which enables us to compute the nonlinear term using a pseudo-spectral approach (see [fourier module](Sources/fourier)).
# Each of these libraries must be installed in the `/lib` folder (here `/gyacomo/lib`).
echo " repository cloned"
echo ______________________________________________
#############################################
### 2. Futils installation
# 2.1 - We navigate to our `lib` folder and clone first the `futils` library.
echo -- 2. Installing Futils
echo "2. Installing Futils"
cd lib
git clone https://c4science.ch/diffusion/FUTILS/futils.git > futils_clone.out
echo " clone repository"
git clone https://c4science.ch/diffusion/FUTILS/futils.git &> futils_clone.out
# **Note:** if you do not have the access, contact me and I will provide a .zip file.
# 2.2 - Then, we navigate to the `src` directory.
......@@ -54,7 +63,8 @@ sed -i '37s/.*/OPT = -O3/' Makefile
# **Note:** the Makefile is also assuming that the Hdf5 library path is stored in a `$(HDF5)` variable and that the `mpif90` compiler is defined. If you are on Marconi HPCC, you may have to change line 34 to `F90 = mpiifort` and line 35 to `HDF5 = $(HDF5_HOME)` (having prealably loaded the Hdf5 module)
# 2.4 - We can now compile the library.
make lib
echo " make library.."
make lib &> futils_make_lib.out
# 2.5 - We create necessary directories to store our library files.
mkdir -p include/O
......@@ -63,57 +73,64 @@ mkdir -p lib/O
mkdir -p lib/g
# 2.6 - Time now to install the library (this will put the library files in the previously made directories).
echo -- compiling...
make install > futils_make_install.out
echo " compiling.."
make install &> futils_make_install.out
# 2.7 - We can test now the installation and linkage of futils by typing `make` in `/gyacomo`. The compilation should pass the previously observed error and halt now with an error at the call of `fftw` routines in `src.fourier_mod.F90`.
echo -- ----Futils installed----
cd ../../
echo " Futils installed"
echo ______________________________________________
#############################################
### 3. FFTW3 installation
echo -- 3. Installing FFTW3
echo "3. Installing FFTW3"
echo " download source"
# 3.1 - We download the `fftw` zip directory, unzip it, and navigate to the directory.
wget http://www.fftw.org/fftw-3.3.10.tar.gz > wget_fftw3.out
tar -xvf fftw-3.3.10.tar.gz > tar_fftw3.out
wget http://www.fftw.org/fftw-3.3.10.tar.gz &> wget_fftw3.out
tar -xvf fftw-3.3.10.tar.gz &> tar_fftw3.out
cd fftw-3.3.10
# 3.2 - We configure the installation and make the double-precision version.
echo -- configure double precision mpi...
./configure --enable-mpi --prefix=$PWD > configure_mpi.out
echo -- compile double precision mpi...
make > make.out
echo " configure double precision mpi.."
./configure --enable-mpi --prefix=$PWD &> configure_mpi.out
echo " compile double precision mpi.."
make &> make.out
# 3.3 - We can now install it.
echo -- installing...
make install > make_install.out
echo " installing.."
make install &> make_install.out
# 3.4 - For single-precision runs, we also configure and install the single-precision version.
echo -- configure single precision mpi...
./configure --enable-float --enable-mpi --prefix=$PWD > configure_float.out
echo -- compile single precision mpi...
make > make_float.out
echo -- installing...
make install > make_install_float.out
echo " configure single precision mpi.."
./configure --enable-float --enable-mpi --prefix=$PWD &> configure_float.out
echo " compile single precision mpi.."
make &> make_float.out
echo " installing.."
make install &> make_install_float.out
# 3.5 - We gather the library files in a new `lib` subdirectory.
mkdir lib
cp lib64/* lib/.
cp *.la lib/.
cp -r lib64/* lib/.
cp -r *.la lib/.
# 3.7 - We go back to `/gyacomo` and verify that `FFTW3DIR = $(LIBDIR)/fftw-3.3.10` in `/gyacomo/local/dirs.inc` when `ENVTYPE = Linux`.
cd ../
# 3.8 - We test the installation and linkage by typing `make` in `/gyacomo`. The compilation should halt with an error at the call of `FM` routines in the `src/coeff_mod.F90` file.
echo -- ----FFTW3 installed----
echo " FFTW3 installed"
echo ______________________________________________
#############################################
## 4. FM installation
echo -- ----Installing FM----
echo "4. Installing FM"
# 4.1 - Navigate back to the main `lib` directory (e.g., `/gyacomo/lib/`) and download the zipped folder.
wget https://dmsmith.lmu.build/FM1.4/FM_files.zip > wget_FM.out
echo " download source"
wget https://dmsmith.lmu.build/FM1.4/FM_files.zip &> wget_FM.out
# 4.2 - Unzip and enter the folder.
unzip FM_files.zip > unzip_FM.out
unzip FM_files.zip &> unzip_FM.out
mv FM_files FM
cd FM
......@@ -121,18 +138,24 @@ cd FM
for file in *.f95 ; do cp "$file" "${file%.*}.F90" ; done
# 4.4 - We compile manually (some compilation may take ~5min).
echo '-- compiling... (give it 5min)'
echo " compiling.. (~5min)"
echo " fmsave.."
ifort fmsave.F90 -c -O3
echo " fm.."
ifort fm.F90 -c -O3
echo " fmzm.."
ifort fmzm90.F90 -c -O3
ifort TestFM.F90 -c -O3
ifort SampleFM.F90 -c -O3
ifort fmsave.o fm.o fmzm90.o TestFM.o -o TestFM
ifort fmsave.o fm.o fmzm90.o SampleFM.o -o SampleFM
echo -- done
# echo " TestFM.."
# ifort TestFM.F90 -c -O3
# echo " SampleFM.."
# ifort SampleFM.F90 -c -O3
# echo " building all.."
# ifort fmsave.o fm.o fmzm90.o TestFM.o -o TestFM
# ifort fmsave.o fm.o fmzm90.o SampleFM.o -o SampleFM
echo " ..done"
# 4.5 We can test the installation.
./TestFM
./SampleFM
# ./TestFM &> TestFM.out
# ./SampleFM &> SampleFM.out
# 4.6 The library file is put together and moved to a local `lib` directory.
mkdir lib
......@@ -144,13 +167,40 @@ mkdir mod
mv *.mod mod
cd ../
echo " FM installed"
echo ______________________________________________
#############################################
# 5 compilation of GYACOMO
cd ../
echo -- we now compile the code...
make
echo -- done
echo "5. Compilation of GYACOMO"
make 2>&1 | tee make.out
echo ______________________________________________
#############################################
# 6. setup of a testcase
echo "6. Test case setup"
make new_prob
echo -- ------
echo -- GYACOMO is ready, you can test running it in simulations/problem_01
echo -- ------
\ No newline at end of file
echo "-- GYACOMO is ready --"
echo "you can test running it using:"
echo "cd gyacomo/simulations/problem_01"
echo "mpirun -np 4 ./gyacomo.exe 1 4 1"
echo ______________________________________________
#############################################
# 7. Epilogue
echo "End of the script"
# Record end time
end=$(date +%s)
# Calculate execution time
execution_time=$((end - start))
# Check if execution time is more than a minute
if [ $execution_time -gt 60 ]; then
execution_time_minutes=$((execution_time / 60))
execution_time_seconds=$((execution_time % 60))
echo "Script executed in $execution_time_minutes minute(s) and $execution_time_seconds second(s)."
else
echo "Script executed in $execution_time second(s)."
fi
echo '=============================================='
\ No newline at end of file
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