Commit fe8a0e6b authored by Lukáš Krupčík's avatar Lukáš Krupčík
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# COMSOL Multiphysics
# COMSOL Multiphysics
## Introduction
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......@@ -52,7 +52,7 @@ Sample output:
-- System Read Throughput(MB/s): 4.93 --
-- System Write Throughput(MB/s): 3.43 --
-- System Memory Throughput(MB/s): 8.35 --
---------------------------------------||---------------------------------------
---------------------------------------||---------------------------------------
```
### Pcm-Msr
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......@@ -124,7 +124,7 @@ The following example prints MFLOPS rate of a naive matrix-matrix multiplication
/* Initialize the Matrix arrays */
for ( i=0; i<SIZE*SIZE; i++ ){
mresult[0][i] = 0.0;
matrixa[0][i] = matrixb[0][i] = rand()*(float)1.1;
matrixa[0][i] = matrixb[0][i] = rand()*(float)1.1;
}
/* Setup PAPI library and begin collecting data from the counters */
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......@@ -121,7 +121,7 @@ The source code of this function can be also found in
```
!!! note
You can also add only following line to you ~/.tvdrc file instead of the entire function:
You can also add only following line to you ~/.tvdrc file instead of the entire function:
**source /apps/mpi/openmpi/intel/1.6.5/etc/openmpi-totalview.tcl**
You need to do this step only once.
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......@@ -108,7 +108,7 @@ Compile the above example with
## Running MPI Programs
!!! note
The MPI program executable must be compatible with the loaded MPI module.
The MPI program executable must be compatible with the loaded MPI module.
Always compile and execute using the very same MPI module.
It is strongly discouraged to mix mpi implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors.
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......@@ -29,11 +29,11 @@ There is default stripe configuration for Anselm Lustre filesystems. However, us
!!! note
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns.
Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns.
```bash
$ lfs getstripe dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
```
Example:
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......@@ -138,7 +138,7 @@ Nodes directly connected to the same InifiBand switch can communicate most effic
!!! note
We recommend allocating compute nodes of a single switch when the best possible computational network performance is required to run job efficiently.
Nodes directly connected to the one InifiBand switch can be allocated using node grouping on PBS resource attribute switch.
Nodes directly connected to the one InifiBand switch can be allocated using node grouping on PBS resource attribute switch.
In this example, we request all 9 nodes directly connected to the same switch using node grouping placement.
......
......@@ -41,13 +41,13 @@ On **Windows**, use [PuTTY ssh client](../get-started-with-it4innovations/access
After logging in, you will see the command prompt:
```bash
_____ _
/ ____| | |
| (___ __ _| | ___ _ __ ___ ___ _ __
\___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \
_____ _
/ ____| | |
| (___ __ _| | ___ _ __ ___ ___ _ __
\___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \
____) | (_| | | (_) | | | | | | (_) | | | |
|_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|
http://www.it4i.cz/?lang=en
......
......@@ -80,7 +80,7 @@ To debug a serial code use:
To debug a parallel code compiled with **OpenMPI** you need to setup your TotalView environment:
!!! hint
!!! hint
To be able to run parallel debugging procedure from the command line without stopping the debugger in the mpiexec source code you have to add the following function to your **~/.tvdrc** file.
```bash
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......@@ -518,7 +518,7 @@ The compilation command for this example is:
$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/
```
To see the performance of Intel Xeon Phi performing the DGEMM run the example as follows:
To see the performance of Intel Xeon Phi performing the DGEMM run the example as follows:
```bash
./gemm -d 1
......@@ -715,7 +715,7 @@ The output should be again similar to:
Hello world from process 0 of 4 on host cn207-mic0
```
!!! hint
!!! hint
**"mpiexec.hydra"** requires a file the MIC filesystem. If the file is missing please contact the system administrators.
A simple test to see if the file is present is to execute:
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......@@ -29,7 +29,7 @@ To run octave in batch mode, write an octave script, then write a bash jobscript
mkdir -p /scratch/work/user/$USER/$PBS_JOBID
cd /scratch/work/user/$USER/$PBS_JOBID || exit
# copy input file to scratch
# copy input file to scratch
cp $PBS_O_WORKDIR/octcode.m .
# load octave module
......
......@@ -66,8 +66,8 @@ There is default stripe configuration for Salomon Lustre file systems. However,
Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns.
```bash
$ lfs getstripe dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
$ lfs getstripe dir | filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir | filename
```
Example:
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......@@ -75,7 +75,7 @@ $ ml spider gcc
GCC:
---------------------------------------------------------------------------------
Description:
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/
Versions:
GCC/4.4.7-system
......@@ -118,7 +118,7 @@ $ module spider GCC/6.2.0-2.27
GCC: GCC/6.2.0-2.27
--------------------------------------------------------------------------------------------------------------
Description:
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/
This module can be loaded directly: module load GCC/6.2.0-2.27
......
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