Commit 2d119ecf authored by David Hrbáč's avatar David Hrbáč

Clean UNICODE hard space

parent e61facfb
Pipeline #1730 passed with stages
in 1 minute and 26 seconds
......@@ -95,7 +95,7 @@ $ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I
In this example, we allocate 4 nodes, 16 cores at 2.4GHhz per node.
Intel Turbo Boost Technology is used by default,  you can disable it for all nodes of job by using resource attribute cpu_turbo_boost.
Intel Turbo Boost Technology is used by default, you can disable it for all nodes of job by using resource attribute cpu_turbo_boost.
```bash
$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16 -l cpu_turbo_boost=0 -I
......
......@@ -29,12 +29,12 @@ fi
### Application Modules
In order to configure your shell for  running particular application on Anselm we use Module package interface.
In order to configure your shell for running particular application on Anselm we use Module package interface.
!!! Note "Note"
The modules set up the application paths, library paths and environment variables for running particular application.
We have also second modules repository. This modules repository is created using tool called EasyBuild. On Salomon cluster, all modules will be build by this tool. If you want to use software from this modules repository, please follow instructions in section [Application Modules Path Expansion](environment-and-modules/#EasyBuild).
We have also second modules repository. This modules repository is created using tool called EasyBuild. On Salomon cluster, all modules will be build by this tool. If you want to use software from this modules repository, please follow instructions in section [Application Modules Path Expansion](environment-and-modules/#EasyBuild).
The modules may be loaded, unloaded and switched, according to momentary needs.
......@@ -44,7 +44,7 @@ To check available modules use
$ module avail
```
To load a module, for example the octave module  use
To load a module, for example the octave module use
```bash
$ module load octave
......@@ -58,7 +58,7 @@ To check loaded modules use
$ module list
```
 To unload a module, for example the octave module use
To unload a module, for example the octave module use
```bash
$ module unload octave
......
......@@ -15,17 +15,17 @@ There are four types of compute nodes:
- 180 compute nodes without the accelerator
- 23 compute nodes with GPU accelerator - equipped with NVIDIA Tesla Kepler K20
- 4 compute nodes with MIC accelerator - equipped with Intel Xeon Phi 5110P
- 4 compute nodes with MIC accelerator - equipped with Intel Xeon Phi 5110P
- 2 fat nodes - equipped with 512 GB RAM and two 100 GB SSD drives
[More about Compute nodes](compute-nodes/).
GPU and accelerated nodes are available upon request, see the [Resources Allocation Policy](resources-allocation-policy/).
All these nodes are interconnected by fast InfiniBand network and Ethernet network.  [More about the Network](network/).
All these nodes are interconnected by fast InfiniBand network and Ethernet network. [More about the Network](network/).
Every chassis provides InfiniBand switch, marked **isw**, connecting all nodes in the chassis, as well as connecting the chassis to the upper level switches.
All nodes share 360 TB /home disk storage to store user files. The 146 TB shared /scratch storage is available for the scratch data. These file systems are provided by Lustre parallel file system. There is also local disk storage available on all compute nodes in /lscratch.  [More about Storage](storage/).
All nodes share 360 TB /home disk storage to store user files. The 146 TB shared /scratch storage is available for the scratch data. These file systems are provided by Lustre parallel file system. There is also local disk storage available on all compute nodes in /lscratch. [More about Storage](storage/).
The user access to the Anselm cluster is provided by two login nodes login1, login2, and data mover node dm1. [More about accessing cluster.](shell-and-data-access/)
......@@ -47,8 +47,8 @@ The parameters are summarized in the following tables:
|MIC accelerated|4, cn[204-207]|
|Fat compute nodes|2, cn[208-209]|
|**In total**||
|Total theoretical peak performance  (Rpeak)|94 TFLOP/s|
|Total max. LINPACK performance  (Rmax)|73 TFLOP/s|
|Total theoretical peak performance (Rpeak)|94 TFLOP/s|
|Total max. LINPACK performance (Rmax)|73 TFLOP/s|
|Total amount of RAM|15.136 TB|
|Node|Processor|Memory|Accelerator|
......
Introduction
============
Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15 TB RAM and giving over 94 TFLOP/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 16 cores, at least 64 GB RAM, and 500 GB hard disk drive. Nodes are interconnected by fully non-blocking fat-tree InfiniBand network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](hardware-overview/).
Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15 TB RAM and giving over 94 TFLOP/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 16 cores, at least 64 GB RAM, and 500 GB hard disk drive. Nodes are interconnected by fully non-blocking fat-tree InfiniBand network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](hardware-overview/).
The cluster runs bullx Linux ([bull](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)) [operating system](software/operating-system/), which is compatible with the RedHat [ Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg) We have installed a wide range of software packages targeted at different scientific domains. These packages are accessible via the [modules environment](environment-and-modules/).
......
Job scheduling
==============
Job execution priority
Job execution priority
----------------------
Scheduler gives each job an execution priority and then uses this job execution priority to select which job(s) to run.
Job execution priority on Anselm is determined by these job properties (in order of importance):
Job execution priority on Anselm is determined by these job properties (in order of importance):
1. queue priority
2. fair-share priority
......@@ -16,7 +16,7 @@ Job execution priority on Anselm is determined by these job properties (in orde
Queue priority is priority of queue where job is queued before execution.
Queue priority has the biggest impact on job execution priority. Execution priority of jobs in higher priority queues is always greater than execution priority of jobs in lower priority queues. Other properties of job used for determining job execution priority (fair-share priority, eligible time) cannot compete with queue priority.
Queue priority has the biggest impact on job execution priority. Execution priority of jobs in higher priority queues is always greater than execution priority of jobs in lower priority queues. Other properties of job used for determining job execution priority (fair-share priority, eligible time) cannot compete with queue priority.
Queue priorities can be seen at <https://extranet.it4i.cz/anselm/queues>
......@@ -48,7 +48,7 @@ Eligible time is amount (in seconds) of eligible time job accrued while waiting
Eligible time has the least impact on execution priority. Eligible time is used for sorting jobs with equal queue priority and fair-share priority. It is very, very difficult for eligible time to compete with fair-share priority.
Eligible time can be seen as eligible_time attribute of job.
Eligible time can be seen as eligible_time attribute of job.
### Formula
......
......@@ -41,13 +41,13 @@ In this example, we allocate 4 nodes, 16 cores per node, for 1 hour. We allocate
$ qsub -A OPEN-0-0 -q qnvidia -l select=10:ncpus=16 ./myjob
```
In this example, we allocate 10 nvidia accelerated nodes, 16 cores per node, for  24 hours. We allocate these resources via the qnvidia queue. Jobscript myjob will be executed on the first node in the allocation.
In this example, we allocate 10 nvidia accelerated nodes, 16 cores per node, for 24 hours. We allocate these resources via the qnvidia queue. Jobscript myjob will be executed on the first node in the allocation.
```bash
$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=16 ./myjob
```
In this example, we allocate 10  nodes, 16 cores per node, for 12 hours. We allocate these resources via the qfree queue. It is not required that the project OPEN-0-0 has any available resources left. Consumed resources are still accounted for. Jobscript myjob will be executed on the first node in the allocation.
In this example, we allocate 10 nodes, 16 cores per node, for 12 hours. We allocate these resources via the qfree queue. It is not required that the project OPEN-0-0 has any available resources left. Consumed resources are still accounted for. Jobscript myjob will be executed on the first node in the allocation.
All qsub options may be [saved directly into the jobscript](job-submission-and-execution/#PBSsaved). In such a case, no options to qsub are needed.
......@@ -72,11 +72,11 @@ Specific nodes may be allocated via the PBS
qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16:host=cn171+1:ncpus=16:host=cn172 -I
```
In this example, we allocate nodes cn171 and cn172, all 16 cores per node, for 24 hours.  Consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. The resources will be available interactively.
In this example, we allocate nodes cn171 and cn172, all 16 cores per node, for 24 hours. Consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. The resources will be available interactively.
### Placement by CPU type
Nodes equipped with Intel Xeon E5-2665 CPU have base clock frequency 2.4GHz, nodes equipped with Intel Xeon E5-2470 CPU have base frequency 2.3 GHz (see section Compute Nodes for details).  Nodes may be selected via the PBS resource attribute cpu_freq .
Nodes equipped with Intel Xeon E5-2665 CPU have base clock frequency 2.4GHz, nodes equipped with Intel Xeon E5-2470 CPU have base frequency 2.3 GHz (see section Compute Nodes for details). Nodes may be selected via the PBS resource attribute cpu_freq .
|CPU Type|base freq.|Nodes|cpu_freq attribute|
|---|---|---|---|
......@@ -91,7 +91,7 @@ In this example, we allocate 4 nodes, 16 cores, selecting only the nodes with In
### Placement by IB switch
Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the [Infiniband network](../network/) fat tree topology. Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.
Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the [Infiniband network](../network/) fat tree topology. Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.
Nodes sharing the same switch may be selected via the PBS resource attribute ibswitch. Values of this attribute are iswXX, where XX is the switch number. The node-switch mapping can be seen at [Hardware Overview](../hardware-overview/) section.
......@@ -129,7 +129,7 @@ In the following example, we select an allocation for benchmarking a very specia
-N Benchmark ./mybenchmark
```
The MPI processes will be distributed differently on the nodes connected to the two switches. On the isw10 nodes, we will run 1 MPI process per node 16 threads per process, on isw20  nodes we will run 16 plain MPI processes.
The MPI processes will be distributed differently on the nodes connected to the two switches. On the isw10 nodes, we will run 1 MPI process per node 16 threads per process, on isw20 nodes we will run 16 plain MPI processes.
Although this example is somewhat artificial, it demonstrates the flexibility of the qsub command options.
......@@ -207,8 +207,8 @@ $ check-pbs-jobs --jobid 35141.dm2 --print-job-out
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Print job standard output:
======================== Job start ==========================
Started at    : Fri Aug 30 02:47:53 CEST 2013
Script name   : script
Started at : Fri Aug 30 02:47:53 CEST 2013
Script name : script
Run loop 1
Run loop 2
Run loop 3
......@@ -278,7 +278,7 @@ $ pwd
In this example, 4 nodes were allocated interactively for 1 hour via the qexp queue. The interactive shell is executed in the home directory.
!!! Note "Note"
All nodes within the allocation may be accessed via ssh.  Unallocated nodes are not accessible to user.
All nodes within the allocation may be accessed via ssh. Unallocated nodes are not accessible to user.
The allocated nodes are accessible via ssh from login nodes. The nodes may access each other via ssh as well.
......
......@@ -243,10 +243,10 @@ Users who have undergone the full local registration procedure (including signin
```bash
$ it4ifree
Password:
     PID   Total Used  ...by me Free
   -------- ------- ------ -------- -------
   OPEN-0-0 1500000 400644   225265 1099356
   DD-13-1    10000 2606 2606 7394
PID Total Used ...by me Free
-------- ------- ------ -------- -------
OPEN-0-0 1500000 400644 225265 1099356
DD-13-1 10000 2606 2606 7394
```
By default file system quota is applied. To check the current status of the quota use
......
......@@ -34,6 +34,6 @@ Capacity computing
Use GNU Parallel and/or Job arrays when running (many) single core jobs.
In many cases, it is useful to submit huge (100+) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization. In this chapter, we discuss the the recommended way to run huge number of jobs, including **ways to run huge number of single core jobs**.
In many cases, it is useful to submit huge (100+) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization. In this chapter, we discuss the the recommended way to run huge number of jobs, including **ways to run huge number of single core jobs**.
Read more on [Capacity computing](capacity-computing/) page.
......@@ -29,7 +29,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
### Notes
The job wall clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be  [set manually, see examples](job-submission-and-execution/).
The job wall clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be [set manually, see examples](job-submission-and-execution/).
Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatically. Wall clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).
......@@ -54,55 +54,55 @@ $ rspbs
Usage: rspbs [options]
Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  --get-node-ncpu-chart
                        Print chart of allocated ncpus per node
  --summary             Print summary
  --get-server-details  Print server
  --get-queues          Print queues
  --get-queues-details  Print queues details
  --get-reservations    Print reservations
  --get-reservations-details
                        Print reservations details
  --get-nodes           Print nodes of PBS complex
  --get-nodeset         Print nodeset of PBS complex
  --get-nodes-details   Print nodes details
  --get-jobs            Print jobs
  --get-jobs-details    Print jobs details
  --get-jobs-check-params
                        Print jobid, job state, session_id, user, nodes
  --get-users           Print users of jobs
  --get-allocated-nodes
                        Print allocated nodes of jobs
  --get-allocated-nodeset
                        Print allocated nodeset of jobs
  --get-node-users      Print node users
  --get-node-jobs       Print node jobs
  --get-node-ncpus      Print number of ncpus per node
  --get-node-allocated-ncpus
                        Print number of allocated ncpus per node
  --get-node-qlist      Print node qlist
  --get-node-ibswitch   Print node ibswitch
  --get-user-nodes      Print user nodes
  --get-user-nodeset    Print user nodeset
  --get-user-jobs       Print user jobs
  --get-user-jobc       Print number of jobs per user
  --get-user-nodec      Print number of allocated nodes per user
  --get-user-ncpus      Print number of allocated ncpus per user
  --get-qlist-nodes     Print qlist nodes
  --get-qlist-nodeset   Print qlist nodeset
  --get-ibswitch-nodes  Print ibswitch nodes
  --get-ibswitch-nodeset
                        Print ibswitch nodeset
  --state=STATE         Only for given job state
  --jobid=JOBID         Only for given job ID
  --user=USER           Only for given user
  --node=NODE           Only for given node
  --nodestate=NODESTATE
                        Only for given node state (affects only --get-node*
                        --get-qlist-* --get-ibswitch-* actions)
  --incl-finished       Include finished jobs
--version show program's version number and exit
-h, --help show this help message and exit
--get-node-ncpu-chart
Print chart of allocated ncpus per node
--summary Print summary
--get-server-details Print server
--get-queues Print queues
--get-queues-details Print queues details
--get-reservations Print reservations
--get-reservations-details
Print reservations details
--get-nodes Print nodes of PBS complex
--get-nodeset Print nodeset of PBS complex
--get-nodes-details Print nodes details
--get-jobs Print jobs
--get-jobs-details Print jobs details
--get-jobs-check-params
Print jobid, job state, session_id, user, nodes
--get-users Print users of jobs
--get-allocated-nodes
Print allocated nodes of jobs
--get-allocated-nodeset
Print allocated nodeset of jobs
--get-node-users Print node users
--get-node-jobs Print node jobs
--get-node-ncpus Print number of ncpus per node
--get-node-allocated-ncpus
Print number of allocated ncpus per node
--get-node-qlist Print node qlist
--get-node-ibswitch Print node ibswitch
--get-user-nodes Print user nodes
--get-user-nodeset Print user nodeset
--get-user-jobs Print user jobs
--get-user-jobc Print number of jobs per user
--get-user-nodec Print number of allocated nodes per user
--get-user-ncpus Print number of allocated ncpus per user
--get-qlist-nodes Print qlist nodes
--get-qlist-nodeset Print qlist nodeset
--get-ibswitch-nodes Print ibswitch nodes
--get-ibswitch-nodeset
Print ibswitch nodeset
--state=STATE Only for given job state
--jobid=JOBID Only for given job ID
--user=USER Only for given user
--node=NODE Only for given node
--nodestate=NODESTATE
Only for given node state (affects only --get-node*
--get-qlist-* --get-ibswitch-* actions)
--incl-finished Include finished jobs
```
Resources Accounting Policy
......@@ -110,7 +110,7 @@ Resources Accounting Policy
### The Core-Hour
The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (16 cores) for 1 hour accounts to 16 core-hours. See example in the  [Job submission and execution](job-submission-and-execution/) section.
The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (16 cores) for 1 hour accounts to 16 core-hours. See example in the [Job submission and execution](job-submission-and-execution/) section.
### Check consumed resources
......@@ -122,8 +122,8 @@ User may check at any time, how many core-hours have been consumed by himself/he
```bash
$ it4ifree
Password:
     PID   Total Used  ...by me Free
   -------- ------- ------ -------- -------
   OPEN-0-0 1500000 400644   225265 1099356
   DD-13-1    10000 2606 2606 7394
PID Total Used ...by me Free
-------- ------- ------ -------- -------
OPEN-0-0 1500000 400644 225265 1099356
DD-13-1 10000 2606 2606 7394
```
......@@ -16,8 +16,8 @@ The authentication is by the [private key](../get-started-with-it4innovations/ac
!!! Note "Note"
Please verify SSH fingerprints during the first logon. They are identical on all login nodes:
29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)
d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7 (RSA)
29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)
d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7 (RSA)
Private key authentication:
......@@ -59,7 +59,7 @@ Example to the cluster login:
Data Transfer
-------------
Data in and out of the system may be transferred by the [scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp protocols.  (Not available yet.) In case large volumes of data are transferred, use dedicated data mover node dm1.anselm.it4i.cz for increased performance.
Data in and out of the system may be transferred by the [scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp protocols. (Not available yet.) In case large volumes of data are transferred, use dedicated data mover node dm1.anselm.it4i.cz for increased performance.
|Address|Port|Protocol|
|---|---|---|
......@@ -75,7 +75,7 @@ The authentication is by the [private key](../get-started-with-it4innovations/ac
1TB may be transferred in 1:50h.
To achieve 160MB/s transfer rates, the end user must be connected by 10G line all the way to IT4Innovations and use computer with fast processor for the transfer. Using Gigabit ethernet connection, up to 110MB/s may be expected.  Fast cipher (aes128-ctr) should be used.
To achieve 160MB/s transfer rates, the end user must be connected by 10G line all the way to IT4Innovations and use computer with fast processor for the transfer. Using Gigabit ethernet connection, up to 110MB/s may be expected. Fast cipher (aes128-ctr) should be used.
!!! Note "Note"
If you experience degraded data transfer performance, consult your local network provider.
......@@ -143,13 +143,13 @@ Port forwarding
It works by tunneling the connection from Anselm back to users workstation and forwarding from the workstation to the remote host.
Pick some unused port on Anselm login node  (for example 6000) and establish the port forwarding:
Pick some unused port on Anselm login node (for example 6000) and establish the port forwarding:
```bash
local $ ssh -R 6000:remote.host.com:1234 anselm.it4i.cz
```
In this example, we establish port forwarding between port 6000 on Anselm and port 1234 on the remote.host.com. By accessing localhost:6000 on Anselm, an application will see response of remote.host.com:1234. The traffic will run via users local workstation.
In this example, we establish port forwarding between port 6000 on Anselm and port 1234 on the remote.host.com. By accessing localhost:6000 on Anselm, an application will see response of remote.host.com:1234. The traffic will run via users local workstation.
Port forwarding may be done **using PuTTY** as well. On the PuTTY Configuration screen, load your Anselm configuration first. Then go to Connection-&gt;SSH-&gt;Tunnels to set up the port forwarding. Click Remote radio button. Insert 6000 to Source port textbox. Insert remote.host.com:1234. Click Add button, then Open.
......@@ -170,7 +170,7 @@ First, establish the remote port forwarding form the login node, as [described a
Second, invoke port forwarding from the compute node to the login node. Insert following line into your jobscript or interactive shell
```bash
$ ssh  -TN -f -L 6000:localhost:6000 login1
$ ssh -TN -f -L 6000:localhost:6000 login1
```
In this example, we assume that port forwarding from login1:6000 to remote.host.com:1234 has been established beforehand. By accessing localhost:6000, an application running on a compute node will see response of remote.host.com:1234
......@@ -196,7 +196,7 @@ Once the proxy server is running, establish ssh port forwarding from Anselm to t
local $ ssh -R 6000:localhost:1080 anselm.it4i.cz
```
Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding  to access the [proxy server from compute nodes](#port-forwarding-from-compute-nodes) as well.
Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding to access the [proxy server from compute nodes](#port-forwarding-from-compute-nodes) as well.
Graphical User Interface
------------------------
......
......@@ -48,9 +48,9 @@ echo Machines: $hl
/ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
```
Header of the PBS file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Header of the PBS file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. >Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. >Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def
**License** should be selected by parameter -P (Big letter **P**). Licensed products are the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS Multiphysics)-**Commercial**.
**License** should be selected by parameter -P (Big letter **P**). Licensed products are the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS Multiphysics)-**Commercial**.
[More about licensing here](licensing/)
......@@ -39,9 +39,9 @@ NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
/ansys_inc/v145/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou
```
Header of the pbs file (above) is common and description can be find on [this site](../../resources-allocation-policy/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Header of the pbs file (above) is common and description can be find on [this site](../../resources-allocation-policy/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common Fluent journal file which is attached to the Fluent solver via parameter -i fluent.jou
Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common Fluent journal file which is attached to the Fluent solver via parameter -i fluent.jou
Journal file with definition of the input geometry and boundary conditions and defined process of solution has e.g. the following structure:
......@@ -64,11 +64,11 @@ The appropriate dimension of the problem has to be set by parameter (2d/3d).
fluent solver_version [FLUENT_options] -i journal_file -pbs
```
This syntax will start the ANSYS FLUENT job under PBS Professional using the qsub command in a batch manner. When resources are available, PBS Professional will start the job and return a job ID, usually in the form of *job_ID.hostname*. This job ID can then be used to query, control, or stop the job using standard PBS Professional commands, such as qstat or qdel. The job will be run out of the current working directory, and all output will be written to the file fluent.o *job_ID*.
This syntax will start the ANSYS FLUENT job under PBS Professional using the qsub command in a batch manner. When resources are available, PBS Professional will start the job and return a job ID, usually in the form of *job_ID.hostname*. This job ID can then be used to query, control, or stop the job using standard PBS Professional commands, such as qstat or qdel. The job will be run out of the current working directory, and all output will be written to the file fluent.o *job_ID*.
3. Running Fluent via user's config file
----------------------------------------
The sample script uses a configuration file called pbs_fluent.conf  if no command line arguments are present. This configuration file should be present in the directory from which the jobs are submitted (which is also the directory in which the jobs are executed). The following is an example of what the content of pbs_fluent.conf can be:
The sample script uses a configuration file called pbs_fluent.conf if no command line arguments are present. This configuration file should be present in the directory from which the jobs are submitted (which is also the directory in which the jobs are executed). The following is an example of what the content of pbs_fluent.conf can be:
```bash
input="example_small.flin"
......@@ -82,9 +82,9 @@ The following is an explanation of the parameters:
input is the name of the input file.
case is the name of the .cas file that the input file will utilize.
case is the name of the .cas file that the input file will utilize.
fluent_args are extra ANSYS FLUENT arguments. As shown in the previous example, you can specify the interconnect by using the -p interconnect command. The available interconnects include ethernet (the default), myrinet, infiniband, vendor, altix, and crayx. The MPI is selected automatically, based on the specified interconnect.
fluent_args are extra ANSYS FLUENT arguments. As shown in the previous example, you can specify the interconnect by using the -p interconnect command. The available interconnects include ethernet (the default), myrinet, infiniband, vendor, altix, and crayx. The MPI is selected automatically, based on the specified interconnect.
outfile is the name of the file to which the standard output will be sent.
......
ANSYS LS-DYNA
=============
**[ANSYSLS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)** software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern  graphical user environment.
**[ANSYSLS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)** software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.
To run ANSYS LS-DYNA in batch mode you can utilize/modify the default ansysdyna.pbs script and execute it via the qsub command.
......@@ -51,6 +51,6 @@ echo Machines: $hl
/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
```
Header of the PBS file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Header of the PBS file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .**k** file which is attached to the ANSYS solver via parameter i=
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .**k** file which is attached to the ANSYS solver via parameter i=
......@@ -2,7 +2,7 @@ ANSYS MAPDL
===========
**[ANSYS Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.
software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.
To run ANSYS MAPDL in batch mode you can utilize/modify the default mapdl.pbs script and execute it via the qsub command.
......@@ -52,7 +52,7 @@ echo Machines: $hl
Header of the PBS file (above) is common and description can be found on [this site](../../resource-allocation-policy/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allow to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ANSYS solver via parameter -i
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ANSYS solver via parameter -i
**License** should be selected by parameter -p. Licensed products are the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic** AUTODYN)
[More about licensing here](licensing/)
Overview of ANSYS Products
==========================
**[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS Channel partner](http://www.ansys.com/)** for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM)
**[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS Channel partner](http://www.ansys.com/)** for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM)
Anselm provides commercial as well as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of  license or by two letter preposition "**aa_**" in the license feature name. Change of license is realized on command line respectively directly in user's PBS file (see individual products). [ More about licensing here](ansys/licensing/)
Anselm provides commercial as well as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of license or by two letter preposition "**aa_**" in the license feature name. Change of license is realized on command line respectively directly in user's PBS file (see individual products). [ More about licensing here](ansys/licensing/)
To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:
......@@ -13,5 +13,5 @@ To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,
ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.
If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the Anselm directly from the client's Workbench project (see ANSYS RSM service).
If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the Anselm directly from the client's Workbench project (see ANSYS RSM service).
LS-DYNA
=======
[LS-DYNA](http://www.lstc.com/) is a multi-purpose, explicit and implicit finite element program used to analyze the nonlinear dynamic response of structures. Its fully automated contact analysis capability, a wide range of constitutive models to simulate a whole range of engineering materials (steels, composites, foams, concrete, etc.), error-checking features and the high scalability have enabled users worldwide to solve successfully many complex problems. Additionally LS-DYNA is extensively used to simulate impacts on structures from drop tests, underwater shock, explosions or high-velocity impacts. Explosive forming, process engineering, accident reconstruction, vehicle dynamics, thermal brake disc analysis or nuclear safety are further areas in the broad range of possible applications. In leading-edge research LS-DYNA is used to investigate the behavior of materials like composites, ceramics, concrete, or wood. Moreover, it is used in biomechanics, human modeling, molecular structures, casting, forging, or virtual testing.
[LS-DYNA](http://www.lstc.com/) is a multi-purpose, explicit and implicit finite element program used to analyze the nonlinear dynamic response of structures. Its fully automated contact analysis capability, a wide range of constitutive models to simulate a whole range of engineering materials (steels, composites, foams, concrete, etc.), error-checking features and the high scalability have enabled users worldwide to solve successfully many complex problems. Additionally LS-DYNA is extensively used to simulate impacts on structures from drop tests, underwater shock, explosions or high-velocity impacts. Explosive forming, process engineering, accident reconstruction, vehicle dynamics, thermal brake disc analysis or nuclear safety are further areas in the broad range of possible applications. In leading-edge research LS-DYNA is used to investigate the behavior of materials like composites, ceramics, concrete, or wood. Moreover, it is used in biomechanics, human modeling, molecular structures, casting, forging, or virtual testing.
Anselm provides **1 commercial license of LS-DYNA without HPC** support now.
......@@ -31,6 +31,6 @@ module load lsdyna
/apps/engineering/lsdyna/lsdyna700s i=input.k
```
Header of the PBS file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution.html). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Header of the PBS file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution.html). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA **.k** file which is attached to the LS-DYNA solver via parameter i=
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA **.k** file which is attached to the LS-DYNA solver via parameter i=
......@@ -9,7 +9,7 @@ Molpro is a software package used for accurate ab-initio quantum chemistry calcu
License
-------
Molpro software package is available only to users that have a valid license. Please contact support to enable access to Molpro if you have a valid license appropriate for running on our cluster (eg. academic research group licence, parallel execution).
Molpro software package is available only to users that have a valid license. Please contact support to enable access to Molpro if you have a valid license appropriate for running on our cluster (eg. academic research group licence, parallel execution).
To run Molpro, you need to have a valid license token present in " $HOME/.molpro/token". You can download the token from [Molpro website](https://www.molpro.net/licensee/?portal=licensee).
......
......@@ -39,7 +39,7 @@ NWChem is compiled for parallel MPI execution. Normal procedure for MPI jobs app
Options
--------------------
Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) and in the input file set the following directives :
Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) and in the input file set the following directives :
- MEMORY : controls the amount of memory NWChem will use
- SCRATCH_DIR : set this to a directory in [SCRATCH file system](../../storage/storage/#scratch) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, e.g.. "scf direct"
- SCRATCH_DIR : set this to a directory in [SCRATCH file system](../../storage/storage/#scratch) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, e.g.. "scf direct"
......@@ -19,7 +19,7 @@ For information about the usage of Intel Compilers and other Intel products, ple
GNU C/C++ and Fortran Compilers
-------------------------------
For compatibility reasons there are still available the original (old 4.4.6-4) versions of GNU compilers as part of the OS. These are accessible in the search path  by default.
For compatibility reasons there are still available the original (old 4.4.6-4) versions of GNU compilers as part of the OS. These are accessible in the search path by default.
It is strongly recommended to use the up to date version (4.8.1) which comes with the module gcc:
......@@ -69,12 +69,12 @@ Simple program to test the compiler
#include <stdio.h>
int main() {
  if (MYTHREAD == 0) {
    printf("Welcome to GNU UPC!!!n");
  }
  upc_barrier;
  printf(" - Hello from thread %in", MYTHREAD);
  return 0;
if (MYTHREAD == 0) {
printf("Welcome to GNU UPC!!!n");
}
upc_barrier;
printf(" - Hello from thread %in", MYTHREAD);
return 0;
}
```
......@@ -115,12 +115,12 @@ Example UPC code:
#include <stdio.h>
int main() {
  if (MYTHREAD == 0) {
    printf("Welcome to Berkeley UPC!!!n");
  }
  upc_barrier;
  printf(" - Hello from thread %in", MYTHREAD);
  return 0;
if (MYTHREAD == 0) {
printf("Welcome to Berkeley UPC!!!n");
}
upc_barrier;
printf(" - Hello from thread %in", MYTHREAD);
return 0;
}
```
......
......@@ -20,7 +20,7 @@ Execution
On the Anselm cluster COMSOL is available in the latest stable version. There are two variants of the release:
- **Non commercial** or so called **EDU variant**, which can be used for research and educational purposes.
- **Commercial** or so called **COM variant**, which can used also for commercial activities. **COM variant** has only subset of features compared to the **EDU variant** available. More about licensing will be posted here soon.
- **Commercial** or so called **COM variant**, which can used also for commercial activities. **COM variant** has only subset of features compared to the **EDU variant** available. More about licensing will be posted here soon.
To load the of COMSOL load the module
......@@ -50,7 +50,7 @@ To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user ca
#PBS -l select=3:ncpus=16
#PBS -q qprod
#PBS -N JOB_NAME
#PBS -A  PROJECT_ID
#PBS -A PROJECT_ID
cd /scratch/$USER/ || exit
......@@ -72,7 +72,7 @@ comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tm
Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).
LiveLink™* *for MATLAB®^
LiveLink™* *for MATLAB®^
-------------------------
COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL**®** API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB.
......@@ -96,7 +96,7 @@ To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you
#PBS -l select=3:ncpus=16
#PBS -q qprod
#PBS -N JOB_NAME
#PBS -A  PROJECT_ID
#PBS -A PROJECT_ID
cd /scratch/$USER || exit
......
......@@ -31,7 +31,7 @@ CUBE is a graphical application. Refer to Graphical User Interface documentation
!!! Note "Note"
Analyzing large data sets can consume large amount of CPU and RAM. Do not perform large analysis on login nodes.
After loading the appropriate module, simply launch cube command, or alternatively you can use scalasca -examine command to launch the GUI. Note that for Scalasca datasets, if you do not analyze the data with scalasca -examine before to opening them with CUBE, not all performance data will be available.
After loading the appropriate module, simply launch cube command, or alternatively you can use scalasca -examine command to launch the GUI. Note that for Scalasca datasets, if you do not analyze the data with scalasca -examine before to opening them with CUBE, not all performance data will be available.
References
1. <http://www.scalasca.org/software/cube-4.x/download.html>
......
......@@ -58,4 +58,4 @@ Vampir is a GUI trace analyzer for traces in OTF format.
$ vampir
```
Read more at the [Vampir](../../salomon/software/debuggers/vampir/) page.
Read more at the [Vampir](../../salomon/software/debuggers/vampir/) page.