update amica

code/plugins/reformat_plugin.py

@@ -32,6 +32,7 @@ def reformat_plugin_dir(plugin_input_dir, plugin_name, order, plugin_type='wiki'
         for file in files:
             if file.endswith('.jpg') or file.endswith('.png'):
                 shutil.copyfile(os.path.join(root, file), os.path.join(plugin_output_dir, file))
+
     # if plugin is 'imat', copy the Docs directory recursively to the output directory
     if plugin_name == 'imat':
         shutil.copytree(os.path.join(plugin_input_dir, 'Docs'), os.path.join(plugin_output_dir, 'Docs'), dirs_exist_ok=True)
@@ -57,6 +58,13 @@ def reformat_plugin_dir(plugin_input_dir, plugin_name, order, plugin_type='wiki'
 
     if plugin_type == 'wiki':
         wiki_plugin_input_dir = plugin_input_dir + '.wiki'
+
+        # copy all .jpg and .png files from wiki input to output dir
+        for root, dirs, files in os.walk(wiki_plugin_input_dir):
+            for file in files:
+                if file.endswith('.jpg') or file.endswith('.png'):
+                    shutil.copyfile(os.path.join(root, file), os.path.join(plugin_output_dir, file))
+
         for root, dirs, files in os.walk(wiki_plugin_input_dir):
             for file in files:
                 if file.endswith('.md') and not file.startswith('index') and not file.startswith('Home'):

code/plugins/update_plugins.py

@@ -36,8 +36,8 @@ def update_repo(repo, order, plugin_type='readme'):
     # if 'github' not in current directory, create it
     if not os.path.exists('github'):
         os.makedirs('github')
-    wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata']
-    readme_plugins = ['ARfitStudio', 'roiconnect', 'EEG-BIDS', 'trimOutlier', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'amica', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
+    wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata', 'amica']
+    readme_plugins = ['ARfitStudio', 'roiconnect', 'EEG-BIDS', 'trimOutlier', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
     ordering = ['ICLabel', 'dipfit', 'EEG-BIDS', 'roiconnect', 'amica', 'cleanline', 'clean_rawdata', 'SIFT', 'zapline-plus', 'eegstats', 'trimOutlier', 'fMRIb', 'imat', 'nwbio', 'NIMA', 'PACT', 'NFT', 'PACTools', 'ARfitStudio', 'PowPowCAT', 'relica', 'std_dipoleDensity', 'viewprops', 'firfilt', 'groupSIFT', 'get_chanlocs', 'nsgportal']
 
     if len(sys.argv) == 1:

plugins/amica/AMICA-Compilation-instructions.md

@@ -0,0 +1,103 @@
+---
+layout: default
+title: AMICA-Compilation-instructions
+long_title: AMICA-Compilation-instructions
+parent: amica
+grand_parent: Plugins
+---
+# How to compile with Intel Fortran on Windows
+
+1. Install Intel OneAPI Base Toolkit for Windows.
+2. Install Intel OneAPI HPC Toolkit for Windows.
+3. Open Intel OneAPI command window (in Start menu, 32 or 64 bit as appropriate). Change to directory with Amica code, and compile Amica with the command (/F sets the stack size):
+
+         > mpif90 /Qopenmp /Qmkl /F2147483648 /DMKL /fpp /O3 /exe:amica15mkl.exe funmod2.f90 amica15.f90
+
+4. Test:
+
+         > .\amica15mkl.exe .\amicadefs.param
+
+5. The files impi.dll and libfabric.dll should be copied to executable folder when running outside OneAPI command window. Search OneAPI mpi directory for locations.
+
+
+# THow to compile with Intel Fortran on Mac
+
+0. These are old instructions. Try using Intel OneAPI modifiying the commands similar to the instructions for Windows above.
+1. Install Intel Fortran compiler for Mac/Linux (free demo).
+   See https://software.intel.com/en-us/intel-parallel-studio-xe
+
+2. Compile MPICH2 setting environmental vars CC, CXX, FC, and F77 to icc and ifort. Set $FBIN to Intel Fortran bin directory.
+
+   i) Download the mpich-3.2 code from: http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
+
+   ii) Compile mpich-3.2:
+
+         $ cp /Users/$USER/downloads/mpich-3.2.tar.gz .   
+         $ setenv CC $FBIN/icc
+         $ setenv CXX $FBIN/icc
+         $ setenv F77 $FBIN/ifort
+         $ setenv FC $FBIN/ifort   
+         $ tar xvf mpich-3.2.tar.gz   
+         $ cd mpich-3.2   
+         $ ./configure --prefix=/Users/$USER/mpich-3.2-install   
+         $ make   
+         $ make install
+
+3. Compile Amica with the command:
+
+         $ ~/mpich-3.2-install/bin/mpif90 -L/Users/$USER/mpich-3.2-install/lib/ -I/Users/$USER/mpich-3.2-install/include/ -qopenmp -mkl -static-intel -O3 -fpp -DMKL amica15.f90 funmod2.f90 -o amica15mac
+
+4. Test:
+
+   i) Download Sample EEG Data (Memorize.fdt and amicadefs.param) from: https://sccn.ucsd.edu/~jason/amica_web.html
+
+   ii) Test binary:
+
+         $ ./amica15mac ./amicadefs.param
+
+
+# How to compile with Intel Fortran on Ubuntu
+
+0. These are old instructions. Try using Intel OneAPI modifiying the commands similar to the instructions for Windows above.
+1. Install Intel Fortran compiler for Linux.
+2. Compile MPICH2 setting environmental vars CC, CXX, FC, and F77 to icc and ifort.
+3. Compile Amica with the command:
+
+         $ /home/jason/mpich2-3.2-install/bin/mpif90 -I/opt/intel/mkl/include/ -fpp -qopenmp -O3 -mkl -static -static-intel -DMKL funmod2.f90 amica15.f90 -o amica15ub
+
+4. Test:
+
+         $ ./amica15ub ./amicadefs.param
+
+
+# How to compile with Intel Fortran on Expanse HPC
+
+1. load appropriate modules:
+
+```
+   module purge
+   module load cpu/0.15.4 intel intel-mkl mvapich2
+```
+
+2. Compile Amica with the command:
+
+```
+   mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays \
+       -qopenmp -mkl -DMKL -o amica15ex funmod2.f90 amica17.f90
+```
+
+3. Test:
+```
+   $ ./amica17nsg ./amicadefs.param
+```
+
+4. Run on compute partition:
+
+```
+   <Edit amicadefs.param file line to: maxthreads 4>
+   $ module load cpu/0.15.4 slurm intel intel-mkl mvapich2
+   $ export OMP_NUM_THREADS=4 ; export SRUN_CPUS_PER_TASK=4 ; export MV2_ENABLE_AFFINITY=0
+   $ srun --partition=compute --nodes=<NUM_NODES> --tasks-per-node=32 --cpus-per-task=4 \
+        --mem=249208M --account=<ACCOUNT> --export=ALL -t 04:00:00 ./amica17nsg ./amicadefs.param
+   <If job fails, reduce block_size in amicadefs.param. Increase block_size to speed up.>
+```