The basic version of MASKE only requires the LAMMPS submodule. If you want to include speciation in your simulation, than you need LAMMPS and PHREEQC. If you want to have bacteria too, you need LAMMPS, PHREEQC, and NUFEB.
| Name | Description | Version |
|---|---|---|
| Git | Distributed version control system | Most recent versions should work |
| CMake | Cross-platform build tool | 3.10 or above (same req. as LAMMPS) |
| MPI | Implementation of the MPI standard | Same requirements as LAMMPS |
Use:
$ cd <path>
$ git clone https://github.com/emasoero/MASKE
$ cd MASKE
$ git submodule update --init lammpspath should be the place where you want the source code to be downloaded.
Same as basic MASKE since PHREEQC doesn't have a git repository.
Use:
$ cd <path>
$ git clone --recurse-submodules https://github.com/emasoero/MASKEIf you get the error:
fatal: repository 'https://github.com/live-clones/hdf5/' not found
fatal: clone of 'https://github.com/live-clones/hdf5' into submodule path '/home/dt/test/MASKE/NUFEB/thirdparty/hdf5' failedignore it since we don't rely on NUFEB's HDF5 output files.
We rely on CMake to provide cross-platform build support.
First we compile LAMMPS. From within the MASKE folder, use:
$ cd lammps
$ mkdir build
$ cd build
$ cmake -DCMAKE_BUILD_TYPE=Release -DWITH_JPEG=Off -DWITH_PNG=Off -DWITH_FFMPEG=Off -DBUILD_LIB=On -DBUILD_OMP=Off -DPKG_MISC=yes -DPKG_USER-MASKE=yes ../cmake
$ make -j
$ cd ../..
$ mkdir buildNB: The -DBUILD_LIB=On option might be obsolete as of 1 Jan 2021. The -j option after make can be removed if that step is unsuccesful (that option is for a faster compilation in parallel, but sometimes it fails on MacOS).
CMake will automatically detect support for MPI in your system. If might fail to detect it (usually when you have a custom MPI installation) so you might need to add -DBUILD_MPI=On and -DMPI_CXX_COMPILER=
If you want to install NUFEB, disregard the box below and move to the section "Enabling NUFEB" below.
If you want to install MASKE without NUFEB, Use:
$ cd build
$ cmake -DCMAKE_BUILD_TYPE=Release ..
$ make -jIf you want to enable speciation by PHREEQC, add the cmake option -DWITH_SPECIATION=On
You will need first to load the required modules:
$ module load CMake
$ module load OpenMPIThen follow the Linux build instructions.
Download PHREEQC source code, uncompress, build and install it using:
$ cd <path where PHREEQC was downloaded>
$ tar -xvzf iphreeqc-3.6.2-15100.tar.gz
$ mkdir build
$ cd build
$ ../configure --prefix=<path to MASKE>/lib/iphreeqc
$ make -j
$ make installThe PHREEQC library files (libiphreeqc.so, etc.) should be installed into MASKE's lib folder.
MASKE can be coupled with microbial simulation provided by LAMMPS's NUFEB module. Optionally, it is possible to enable NUFEB with VTK support to output .vti and .vtu files for grid based data and per-atom data. You can use those files to visualise the simulation using Paraview. For more information on how to generate those files plase refer to the NUFEB user manual.
Use the following build steps:
$ cd NUFEB
$ mkdir build
$ cd build
$ cmake -DCMAKE_BUILD_TYPE=Release -DWITH_NUFEB=On ..You will get an CMake error after this but just ignore it.
$ cd ../NUFEBIf you don't want to enable VTK support do:
$ ./install.sh --enable-misc --static
$ cd ../build
$ cmake -DCMAKE_BUILD_TYPE=Release -DWITH_NUFEB=On ..Otherwise do:
$ ./install.sh --enable-misc --enable-vtk --static
$ cd ../build
$ cmake -DCMAKE_BUILD_TYPE=Release -DWITH_NUFEB=On -DWITH_VTK=On -DVTK_DIR=$PWD/../NUFEB/thirdparty/vtk/vtk-build ..Finally, compile MASKE using:
$ make -jAfter build is completed the MASKE folder should contain the following folders:
$ cd MASKE
$ ls| Folder | Description |
|---|---|
| src | Source files |
| lib | Library dependancies files |
| tests | Collection of test cases |
| bin | Built executables |
| lammps | LAMMPS source folder |
In the build folder type the following command:
$ cmake -DMPI_CXX_COMPILER=<path> ..
$ make -jwith path being the path to the desired MPI compiler.
If you are trying to compile LAMMPS when you get the error, in the lammps/build folder type the following command:
$ cmake -DCMAKE_CXX_FLAGS="-std=c++11" ../cmake
$ make -jIf you are trying to compile MASKE, in the MASKE/build folder type the following command:
$ cmake -DCMAKE_CXX_FLAGS="-std=c++11" ..
$ make -jmake -j can sometimes create problems. Try using only make, without the -j optionLet's try running an example located at the tests folder:
$ cd tests/test12-Lay_Nucl_2Grp_Sm_Mono_1pr
$ mpiexec -np 4 ../../build/maske input_read.dat Follow the instructions on the Rocket webpage. For a quick interactive run do:
$ cd tests/test12-Lay_Nucl_2Grp_Sm_Mono_1pr
$ srun -p interactive -n 4 --pty /bin/bash
$ mpiexec -np 4 ../../build/maske input_read.dat This section explains how to update LAMMPS to the current version in the MASKE distribution
Go to the MASKE/lammps folder
$ git checkout user_maske
$ git pullThen compil LAMMPS as previously exlained.
This section explains how you can choose a version of LAMMPS different from what is included in the MASKE distribution (e.g., the latest one).
Go to the MAKSE/lammps folder
$ git remote add upstream git@github.com:lammps/lammps.gitNow, with git remote -v you should see origin and upstream. Then:
$ git checkout user_maske
$ git fetch upstream
$ git merge <tag_name>You can find the
Then git status shows conflict as files that have been both modified. Opening the files with conflicts, look for <<<<<<< HEAD for what is in the local version, and >>>>>>>> <tag_name> for what is in the file you pulled from LAMMPS. Typically, you should keep everything that is in the newer version of LAMMPS, while adding the parts that are specific to the USER_MASKE package we created. When done, git status should not show conflicts anymore.
Then compile LAMMPS as explained previously.
If you are a Developer and want to upgrade the LAMMPS version in MASKE on Github, you also need to follow the steps below, while in MASKE/lammps:
$ git commit -m "<your_message>"
$ git pushThen go to the MASKE folder and type:
$ git add lammps
$ git commit -m “<your message>
$ git push