home.md

@@ -234,12 +234,14 @@ The setup is already described with the Linux client.
 module av
 
 ----------------------------------------------------------------------------------------------- /share/modulefiles ------------------------------------------------------------------------------------------------
-   BRAINimaging/fsl/fsleyes    BRAINimaging/fsl/5.0.9     BRAINimaging/fsl/6.0.3 (D)    library/cuda/9.1                        mpi/mpich/3.3.2/gcc-8.2.1       singularity/3.4.2
-   BRAINimaging/fsl/fslview    BRAINimaging/fsl/5.0.10    MATLAB/R2018b                 library/cuda/9.2                        mpi/openmpi/3.1.5/gcc-8.2.1     singularity/3.5.1              (D)
-   BRAINimaging/fsl/5.0.4      BRAINimaging/fsl/5.0.11    MATLAB/R2019b          (D)    library/cuda/10.0                       mpi/openmpi/4.0.2/gcc-8.2.1     system/hwloc/1.11.13/gcc-8.2.1
-   BRAINimaging/fsl/5.0.6      BRAINimaging/fsl/6.0.0     library/cuda/7.5              library/cuda/10.1                       pmi/openpmix/2.2.3/gcc-8.2.1    system/hwloc/2.1.0/gcc-8.2.1
-   BRAINimaging/fsl/5.0.7      BRAINimaging/fsl/6.0.1     library/cuda/8.0              library/cuda/10.2                (D)    pmi/openpmix/3.1.4/gcc-8.2.1    system/knem/1.1.3/gcc-8.2.1
-   BRAINimaging/fsl/5.0.8      BRAINimaging/fsl/6.0.2     library/cuda/9.0              library/openblas/0.3.7/gcc-8.2.1        pmi/openpmix/4.0.0/gcc-8.2.1
+   MATLAB/R2018b                                    NeuroImaging/fsl/5.0.9             Pharmaceutical/pirana/2.9.8 (D)    library/cuda/10.2                (D)    singularity/3.4.2
+   MATLAB/R2019b                             (D)    NeuroImaging/fsl/5.0.10            library/cuda/7.5                   library/openblas/0.3.7/gcc-8.2.1        singularity/3.5.1              (D)
+   NeuroImaging/freesurfer/stable-pub-v6.0.0        NeuroImaging/fsl/5.0.11            library/cuda/8.0                   mpi/mpich/3.3.2/gcc-8.2.1               system/hwloc/1.11.13/gcc-8.2.1
+   NeuroImaging/fsl/fsleyes                         NeuroImaging/fsl/6.0.0             library/cuda/9.0                   mpi/openmpi/3.1.5/gcc-8.2.1             system/hwloc/2.1.0/gcc-8.2.1
+   NeuroImaging/fsl/5.0.4                           NeuroImaging/fsl/6.0.1             library/cuda/9.1                   mpi/openmpi/4.0.2/gcc-8.2.1      (L)    system/knem/1.1.3/gcc-8.2.1
+   NeuroImaging/fsl/5.0.6                           NeuroImaging/fsl/6.0.2             library/cuda/9.2                   pmi/openpmix/2.2.3/gcc-8.2.1
+   NeuroImaging/fsl/5.0.7                           NeuroImaging/fsl/6.0.3      (D)    library/cuda/10.0                  pmi/openpmix/3.1.4/gcc-8.2.1
+   NeuroImaging/fsl/5.0.8                           Pharmaceutical/pirana/2.9.7        library/cuda/10.1                  pmi/openpmix/4.0.0/gcc-8.2.1
 
 ---------------------------------------------------------------------------------------- /share/software/easybuild/modules ----------------------------------------------------------------------------------------
    all/EasyBuild/4.0.1    tools/EasyBuild/4.0.1
@@ -248,6 +250,7 @@ module av
    lmod    settarg
 
   Where:
+   L:  Module is loaded
    D:  Default Module
 
 Use "module spider" to find all possible modules and extensions.
@@ -279,7 +282,7 @@ module purge
 ```
 
 ## Compiling programs
-- vi hello1.c
+- vi hello.c
 
 ```
 #include <stdio.h>
@@ -297,7 +300,7 @@ int main (int argc, char *argv[])
   MPI_Comm_rank (MPI_COMM_WORLD, &id);
   MPI_Get_processor_name (processor_name, &processor_name_len);
 
-  for (i=1;i<2;i++)
+  for (i=1; i<2; i++)
     printf ("Hello world from process %03d out of %03d, processor name %s \n", id, np, processor_name);
 
   MPI_Finalize ();
@@ -305,15 +308,15 @@ int main (int argc, char *argv[])
 }
 ```
 
-- mpicc hello1.c -o hello1
+- mpicc hello.c -o hello
 
-- ./hello1
+- ./hello
 
 ```
 Hello world from process 000 out of 001, processor name res-hpc-lo01.researchlumc.nl
 ```
 
-- mpirun ./hello1
+- mpirun ./hello
 
 ```
 Hello world from process 003 out of 016, processor name res-hpc-lo01.researchlumc.nl 
@@ -333,70 +336,13 @@ Hello world from process 008 out of 016, processor name res-hpc-lo01.researchlum
 Hello world from process 009 out of 016, processor name res-hpc-lo01.researchlumc.nl 
 Hello world from process 014 out of 016, processor name res-hpc-lo01.researchlumc.nl
 ```
-- vi hello2.c
-
-```
-#include "mpi.h"
-#include "string.h"
-#include <stdio.h>
-
-int main (int argc, char *argv[])
-{
-  int numprocs, myrank, namelen, i;
-  char processor_name[MPI_MAX_PROCESSOR_NAME];
-  char greeting[MPI_MAX_PROCESSOR_NAME + 80];
-  MPI_Status status;
-
-  MPI_Init (&argc, &argv);
-  MPI_Comm_size (MPI_COMM_WORLD, &numprocs);
-  MPI_Comm_rank (MPI_COMM_WORLD, &myrank);
-  MPI_Get_processor_name (processor_name, &namelen);
-
-  sprintf (greeting, "Hello world, from process %d of %d on %s", myrank, numprocs, processor_name);
-
-  if (myrank == 0)
-    {
-     printf ("%s\n", greeting);
-     for (i = 1; i < numprocs; i++ )
-       {
-        MPI_Recv (greeting, sizeof (greeting), MPI_CHAR, i, 1, MPI_COMM_WORLD, &status);
-        printf ("%s\n", greeting);
-      }
-    }
-  else
-    MPI_Send (greeting, strlen (greeting) + 1, MPI_CHAR, 0, 1, MPI_COMM_WORLD);
-
-  MPI_Finalize ();
-  return 0;
-}
-```
-
-- mpicc hello2.c -o hello2
-
-- ./hello2
-
-```
-Hello world, from process 0 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 1 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 2 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 3 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 4 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 5 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 6 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 7 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 8 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 9 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 10 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 11 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 12 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 13 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 14 of 16 on res-hpc-lo01.researchlumc.nl
-Hello world, from process 15 of 16 on res-hpc-lo01.researchlumc.nl
-```
 
 ## Submitting jobs
 
 ```
+module purge
+module add mpi/openmpi/4.0.2/gcc-8.2.1
+
 git clone https://github.com/intel/mpi-benchmarks
 cd mpi-benchmarks
 make clean