Differences between revisions 9 and 44 (spanning 35 versions)

CLaMS Installation

Download Source Code

The CLaMS source code can be downloaded from the Gitlab server https://jugit.fz-juelich.de.

To get full read and write access to the complete CLaMS code on the gitlab server, one needs to be registered by the server (login once) and then given access by the maintainer Nicole Thomas (n.thomas@fz-juelich.de).

Access to Jugit via ssh or https, see Access to Jugit and Gitlab

For registered users CLaMS is available here:

git clone git@jugit.fz-juelich.de:clams/clams-git.git [target-directory]

Without any registration CLaMS can be downloaded with:

git clone https://jugit.fz-juelich.de/clams/clams-git.git [target-directory]

This version contains all modules, libraries and programs needed for a classical CLaMS simulation employing a ksh-script. It does not include supplementary programs e.g. needed for the conversion of the meteorological data.

Example input data can be downloaded by:

git clone https://jugit.fz-juelich.de/clams/clams-test-data.git [target-directory]

Some additional CLaMS packages can be downloaded by registered users as follows:

git clone git@jugit.fz-juelich.de:clams/clams-support.git [target-directory]

At the moment ssh agent forwarding to JURECA/JUWELS is not allowed and outgoing ssh communication from these systems is blocked.

The source code can only be downloaded via https to JURECA or JUWELS:

git clone https://jugit.fz-juelich.de/clams/clams-git.git [target-directory]

git clone https://jugit.fz-juelich.de/clams/clams-support.git [target-directory]

Compilation

Requirements are a Fortran compiler and a NetCDF library with a Fortran interface and optionally an MPI library.
The Intel compiler and the MPICH library are used by default in the ICE4 cluster.
On JUWELS, the Intel compiler is used with the ParaStationMPI library.
The use of gfortran is also possible, both on ICE4 cluster machines and on Juwels.
For other computer systems or other compilers, adjustments may need to be made in the makefiles under mkincl.

For compilation of all CLaMS programs, go to the target directory and simply type:

```
make all 
```

If you already have a pre-installed version, you must clean it up before the compilation:

```
make distclean 
```

For compilation of a specific program progname in package package-name:

cd target-directory
make libs
cd package-name
make progname

The source code is compiled with MPI by default. The created executables can be run serially or in parallel. Please make sure, that mpif90 can be used or switch it off (see below).

On ICE-4 workstations with Ubuntu 24.04 the Intel compiler ifx must be made available and the bin subdirectory of the installation directory of MPICH library must be added to your path:

source /opt/intel/oneapi/setvars.sh

PATH=/usr/nfs/software/icg1/local/mpich-4.3.1-ifx-2024.2.0/bin:$PATH
export PATH

If the gfortran compiler is used on ICE-4 workstations and MPI support is required the PATH must be set to:

PATH=/usr/nfs/software/icg1/local/mpich-4.3.1-gfortran-13.3.0/bin:$PATH
export PATH

Under Ubuntu 20.04 (icg1220) the Intel compiler ifort is automatically available, but the corresponding MPICH directory must be added to your path:

PATH=/usr/nfs/software/icg1/local/mpich-3.3.2-ifort-19.0.8/bin:$PATH
export PATH

For compilation and execution on the supercomputers JURECA/JUWELS see: https://clams.icg.kfa-juelich.de/CLaMS/Jureca/CompileExecute

It is possible to compile without MPI, switch to gfortran compiler or use debug options with:

make [noMPI=true] [useComp=gfortran] [isDebug=true] [useSHM=true] all|libs|package-name

Option	Default
noMPI	false	switch to true to compile without MPI
useComp	ifc (intel fortran compiler)	switch to gfortran to compile with gfortran compiler
isDebug	false	switch to true to use debug options for compiling
useSHM	false	switch to true to use MPI3 Shared Memory and Parallel IO (only implemented for intel compiler on JUWELS) (only used for meteorological data in traj)

-  ⇤ ← Revision 9 as of 2019-04-04 06:31:30 → 
  Size: 1216
  Editor: JensUweGrooss
  Comment:
+   ← Revision 44 as of 2025-07-14 08:58:56 → ⇥
  Size: 4652
  Editor: NicoleThomas
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+#acl ClamsUserGroup:read,write,delete,revert All:read
-Line 3:
+Line 5:
-The CLaMS source code can be downloaded from the GitLab server https://jugit.fz-juelich.de.
+== Download Source Code ==

The CLaMS source code can be downloaded from the Gitlab server https://jugit.fz-juelich.de.

To get full read and write access to the complete CLaMS code on the gitlab server, one needs to be registered by the server (login once) and then given access by the maintainer Nicole Thomas (n.thomas@fz-juelich.de). 

Access to ''Jugit'' via ssh or https, see [[ AccessJugit | Access to Jugit and Gitlab ]]


For registered users CLaMS is available here:
 {{{
git clone git@jugit.fz-juelich.de:clams/clams-git.git [target-directory]
}}}

Without any registration CLaMS can be downloaded with:
 {{{
git clone https://jugit.fz-juelich.de/clams/clams-git.git [target-directory]
}}}
-Line 7:
+Line 26:
-To download the CLaMS code from the gitlab server, one needs to be registered by the server (login once) and then given access by the maintainer Nicole Thomas (n.thomas@fz-juelich.de). The ssh keys should be uploaded to the GitLab Server. Then the code of the CLaMS version 2.0 can be downloaded by
-Line 9:
+Line 27:
-{{{
git clone https://clams.icg.kfa-juelich.de:clams/CLaMS.git [target-directory]
+Example input data can be downloaded by:
 {{{
git clone https://jugit.fz-juelich.de/clams/clams-test-data.git [target-directory]
-Line 13:
+Line 32:
-Respectively, internally the develop version is available here:
{{{
git clone git@jugit.fz-juelich.de:clams/clams-git.git [target-directory]
+Some additional CLaMS packages can be downloaded by registered users as follows:
 {{{
git clone git@jugit.fz-juelich.de:clams/clams-support.git [target-directory]
-Line 18:
+Line 37:
-For compilation of all CLaMS program, go to the target directory and simply type
+'''At the moment ssh agent forwarding to JURECA/JUWELS is not allowed and outgoing ssh communication from these systems is blocked.
-Line 20:
+Line 39:
-{{{
+The source code can only be downloaded via https to JURECA or JUWELS: '''
 {{{
git clone https://jugit.fz-juelich.de/clams/clams-git.git [target-directory]

git clone https://jugit.fz-juelich.de/clams/clams-support.git [target-directory]
}}}


== Compilation ==

 * Requirements are a Fortran compiler and a NetCDF library with a Fortran interface and optionally an MPI library.

 * The Intel compiler and the MPICH library are used by default in the ICE4 cluster. 

 * On JUWELS, the Intel compiler is used with the ParaStationMPI library.

 * The use of gfortran is also possible, both on ICE4 cluster machines and on Juwels.

 * For other computer systems or other compilers, adjustments may need to be made in the makefiles under '''''mkincl'''''.


For compilation of all CLaMS programs, go to the target directory and simply type:
 {{{
-Line 24:
+Line 65:
-Installing on JURECA works identically. If you want to use your ssh-keys from the workstation cluster for downloading the code, you may connect to JURECA by
{{{
ssh -A [-X] <user>@jureca.fz-juelich.de
+If you already have a pre-installed version, you must clean it up before the compilation:
 {{{
make distclean
-Line 28:
+Line 69:
+For compilation of a specific program ''progname'' in package ''package-name'':
 {{{
cd target-directory
make libs
cd package-name
make progname
}}}

The source code is compiled with MPI by default.
The created executables can be run serially or in parallel.
Please make sure, that '''''mpif90''''' can be used or switch it off (see below).

On '''ICE-4 workstations''' with '''Ubuntu 24.04''' the Intel compiler '''ifx''' must be made available and the bin subdirectory of the installation directory of '''MPICH''' library must be added to your path:
  {{{
source /opt/intel/oneapi/setvars.sh

PATH=/usr/nfs/software/icg1/local/mpich-4.3.1-ifx-2024.2.0/bin:$PATH
export PATH
}}}

If the '''gfortran''' compiler is used on '''ICE-4 workstations''' and '''MPI''' support is required the PATH must be set to:
  {{{
PATH=/usr/nfs/software/icg1/local/mpich-4.3.1-gfortran-13.3.0/bin:$PATH
export PATH
}}}



Under '''Ubuntu 20.04 (icg1220)''' the Intel compiler ifort is automatically available, but the corresponding '''MPICH''' directory must be added to your path:
 {{{
PATH=/usr/nfs/software/icg1/local/mpich-3.3.2-ifort-19.0.8/bin:$PATH
export PATH
}}}

For compilation and execution on the supercomputers '''JURECA/JUWELS''' see:
https://clams.icg.kfa-juelich.de/CLaMS/Jureca/CompileExecute


It is possible to compile without MPI, switch to gfortran compiler or use debug options with:
 {{{ 
make [noMPI=true] [useComp=gfortran] [isDebug=true] [useSHM=true] all|libs|package-name
}}}

 || '''Option''' || '''Default''' || ||
 || '''''noMPI'''''   ||''false''                         || switch to ''true'' to compile without MPI ||
 || '''''useComp''''' || ''ifc'' (intel fortran compiler) || switch to ''gfortran'' to compile with gfortran compiler ||
 || '''''isDebug''''' || ''false''                        || switch to ''true'' to use debug options for compiling ||
 || '''''useSHM'''''  || ''false''                        || switch to ''true'' to use MPI3 Shared Memory and Parallel IO <<BR>> (only implemented for intel compiler on JUWELS) <<BR>> (only used for meteorological data in '''traj''') ||