Diff for "ParallelHowTo"

Differences between revisions 2 and 13 (spanning 11 versions)

ParallelHowTo

Contents

ParallelHowTo

It is possible to run CLaMS on multi-processor machines using MPI.

Intel Compiler 11.1

The MPICH2 Library (1.3.2p1) is installed in directory /usr/nfs/local/local/mpich2-intel (for Intel C and Fortran compilers). Add the bin subdirectory of the installation directory to your path:
```
PATH=/usr/nfs/local/local/mpich2-intel/bin:$PATH
export PATH
```
To read the man pages set MANPATH to the following:
```
MANPATH=/usr/nfs/local/local/mpich2-intel/share/man:$MANPATH
export MANPATH
```
The programs can be compiled with:
```
make useComp=ifc useMPI=true <progname>
```
Execute on <n> CPUs:
```
mpiexec -np <n> <progname>
```
It may be necessary to unset the memory limit:
```
ulimit -s unlimited
```

Portland Compiler 10.4

On the Ubuntu machines the PGF compiler suite is installed that has MPICH implemented. In the following a short How to: First it is necessary to make the path of the MPI libraries public by executing:
```
. /opt/pgi/linux86-64/10.4/mpi.sh
```
Then compile the needed programs by executing:
```
make useMPI=true
```
Before running the CLaMS script or a single program you have to execute:
```
> ssh-agent
> SSH_AUTH_SOCK=/tmp/ssh-arHtY17224/agent.17224; export SSH_AUTH_SOCK;
> SSH_AGENT_PID=17225; export SSH_AGENT_PID;
> echo Agent pid 17225;
> ssh-add .ssh/id_rsa
```
This is necessary, because the processes communicate per ssh. The programs must be called as following:
```
mpirun -np # [ --all-local ] program

# - number of processors
use the option --all-local for running it on the CPUs of the local machine only.
```

Intel Compiler 14.0.3

The MPICH Library 3.1.2 is installed in directory /usr/nfs/local/local/mpich-3.1.2-ifort-14.0.3. Add the bin subdirectory of the installation directory of MPICH library to your path:
```
PATH=/usr/nfs/local/local/mpich-3.1.2-ifort-14.0.3/bin:$PATH
export PATH
```
Clams programs can be compiled with:
```
make useMPI=true [useComp=ifc] progname
```
Execute on <n> CPUs:
```
mpiexec|mpirun -np <n> <progname>
```

Portland Compiler 14.6

It is necessary to make the path of the MPI libraries (included in the portland compiler suite) public by executing:
```
. /opt/pgi/linux86-64/14.6/mpi.sh
```
Clams programs can be compiled with:
```
make useMPI=true [useComp=pgi] progname
```
Execute on <n> CPUs:
```
mpiexec|mpirun -np <n> <progname>
```

-  ⇤ ← Revision 2 as of 2011-05-02 12:25:48 → 
  Size: 839
  Editor: GebhardGuenther
  Comment:
+   ← Revision 13 as of 2014-08-29 07:18:38 → ⇥
  Size: 2668
  Editor: NicoleThomas
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+#acl ClamsUserGroup:read,write,delete,revert All:read
-Line 2:
+Line 5:
-= HowToParallel =
+== ParallelHowTo ==
-Line 4:
+Line 7:
-It is possible to run CLaMS on multi-processor machines using MPI or OpenMP.
+<<TableOfContents>>
-Line 6:
+Line 9:
-On the Ubuntu machines is the PGF compiler suite installed that has MPICH implemented.
+It is possible to run CLaMS on multi-processor machines using MPI.
-Line 8:
+Line 11:
-In the following a short How to:
+=== Intel Compiler 11.1 ===
-Line 10:
+Line 13:
-First it is necessary to make the path of the MPI libraries public by executing:
+ The MPICH2 Library (1.3.2p1) is installed in directory ''/usr/nfs/local/local/mpich2-intel'' (for Intel C and Fortran compilers).
-Line 12:
+Line 15:
-for 64bit machines:

{{{
. /opt/pgi/linux86-64/8.0-2/mpi.sh
+ Add the bin subdirectory of the installation directory to your path:
 {{{
PATH=/usr/nfs/local/local/mpich2-intel/bin:$PATH
export PATH
-Line 18:
+Line 21:
-for 32bit machines:

{{{
. /opt/pgi/linux86/8.0-2/mpi.sh
+ To read the man pages set MANPATH to the following:
 {{{
MANPATH=/usr/nfs/local/local/mpich2-intel/share/man:$MANPATH
export MANPATH
-Line 24:
+Line 27:
-Then compile the needed programs by executing:
+ The programs can be compiled with:
 {{{
make useComp=ifc useMPI=true <progname>
}}}
-Line 26:
+Line 32:
-{{{
+ Execute on <n> CPUs:
 {{{
mpiexec -np <n> <progname>
}}}

 It may be necessary to unset the memory limit:
 {{{
ulimit -s unlimited
}}}

=== Portland Compiler 10.4 ===

 On the Ubuntu machines the PGF compiler suite is installed that has MPICH implemented.

 In the following a short How to:

 First it is necessary to make the path of the MPI libraries public by executing:
 {{{
. /opt/pgi/linux86-64/10.4/mpi.sh
}}}

 Then compile the needed programs by executing:
 {{{
-Line 30:
+Line 58:
-Before running the CLaMS script or a single program you have to execute:

{{{
ssh-add
+ Before running the CLaMS script or a single program you have to execute:
 {{{
> ssh-agent
> SSH_AUTH_SOCK=/tmp/ssh-arHtY17224/agent.17224; export SSH_AUTH_SOCK;
> SSH_AGENT_PID=17225; export SSH_AGENT_PID;
> echo Agent pid 17225;
> ssh-add .ssh/id_rsa
-Line 36:
+Line 67:
-This is necessary, because the processes communicate per ssh.
+ This is necessary, because the processes communicate per ssh.
-Line 38:
+Line 69:
-The programs must be called as following:

{{{
mpirun -np # program
+ The programs must be called as following:
 {{{
mpirun -np # [ --all-local ] program
-Line 44:
+Line 74:
+use the option --all-local for running it on the CPUs of the local machine only.
}}}
-Line 45:
+Line 77:
+=== Intel Compiler 14.0.3 ===

 The MPICH Library 3.1.2 is installed in directory ''/usr/nfs/local/local/mpich-3.1.2-ifort-14.0.3''.
 Add the bin subdirectory of the installation directory of MPICH library to your path: 
 {{{
PATH=/usr/nfs/local/local/mpich-3.1.2-ifort-14.0.3/bin:$PATH
export PATH
-Line 46:
+Line 87:
+ Clams programs can be compiled with: 
 {{{
make useMPI=true [useComp=ifc] progname
}}}

 Execute on <n> CPUs:
 {{{
mpiexec|mpirun -np <n> <progname>
}}}

=== Portland Compiler 14.6 ===

 It is necessary to make the path of the MPI libraries (included in the portland compiler suite) public by executing: 
 {{{
. /opt/pgi/linux86-64/14.6/mpi.sh
}}}

 Clams programs can be compiled with: 
 {{{
make useMPI=true [useComp=pgi] progname
}}}

 Execute on <n> CPUs:
 {{{
mpiexec|mpirun -np <n> <progname>
}}}