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./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.html
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View file @ 2c035b8e
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login](https://docs.it4i.cz/salomon/vpn_login.png/@@images/5102f29d-93cf-4cfd-8f55-c99c18f196ea.png "VPN login")](../vpn_login.png)&![](vpn_login.png)
Connection](https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images/45537053-a47f-48b2-aacd-3b519d6770e6.png "VPN Succesfull Connection")](../vpn_successfull_connection.png)&![](vpn_successfull_connection.png)
[![Salomon](https://docs.it4i.cz/salomon/salomon-2/@@images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpeg "Salomon")](../salomon-2)&![Salomon](../salomon-2)&![](salomon-2)
![UV&
2000](../uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg "UV 2000")&![](uv-2000.jpeg)
[![Salomon](https://docs.it4i.cz/salomon/salomon/@@images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpeg "Salomon")](salomon)&![](salomon)
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[![7D_Enhanced_hypercube.png](https://docs.it4i.cz/salomon/network-1/7D_Enhanced_hypercube.png/@@images/03693a91-beec-4d04-bf11-7d89c20420a6.png "7D_Enhanced_hypercube.png")](7D_Enhanced_hypercube.png)&![](7D_Enhanced_hypercube.png)
[![Mcell](ib-single-plane-topology/IBsingleplanetopologyICEXMcellsmall.png "Mcell")](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)&![](IBsingleplanetopologyICEXMcellsmall.png)
[![Accelerated&
nodes](ib-single-plane-topology/IBsingleplanetopologyAcceleratednodessmall.png "Accelerated nodes")](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)&![](IBsingleplanetopologyAcceleratednodessmall.png)
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![](AMsetPar1.png/@@images/a34a45cc-9385-4f05-b12e-efadf1bd93bb.png)&![](AMsetPar1.png)
![Part of report.html](http://verif.cs.vsb.cz/aislinn/doc/report.png)&![](report.png)
[![](ddt1.png){.image-inline width="451"&![](ddt1.png)
height="513"}](ddt1.png)&
![Allinea Reverse&
Connect](Snmekobrazovky20160211v14.27.45.png/@@images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png "Allinea Reverse Connect")&![](Snmekobrazovky20160211v14.27.45.png)
[![screenshot](https://docs.it4i.cz/salomon/software/debuggers/vtune-amplifier/@@images/7ca8748b-69ad-4b53-9667-29c2fdaa8913.png "VTune Amplifier")](vtune-amplifier)&![](vtune-amplifier.png)
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![Intel Trace&
Analyzer](Snmekobrazovky20151204v15.35.12.png/@@images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png "Intel Trace Analyzer")&![](Snmekobrazovky20151204v15.35.12.png)
![The Authorization chain for access and utilization of computational&
resources on&
Anselm](../../anselm-cluster-documentation/Authorization_chain.png "Authorization chain")&![](Authorization_chain.png)
screensaver](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png "Disable lock screen and screensaver")](gdmdisablescreensaver.png)&![](gdmdisablescreensaver.png)
[![gnome-terminal.png](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png/@@images/b44f5d8c-156d-4041-9bb0-973996413834.png "gnome-terminal.png")](gnome-terminal.png)&![](gnome-terminal.png)
[![gnome-compute-nodes-over-vnc.png](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png/@@images/d4c9b6b6-6e2c-48c0-84dd-26d291517355.png "gnome-compute-nodes-over-vnc.png")](gnome-compute-nodes-over-vnc.png)&![](gnome-compute-nodes-over-vnc.png)
![screenshot](vtune-amplifier/@@images/3d4533af-8ce5-4aed-9bac-09fbbcd2650a.png "VTune Amplifier")&![screenshot](vtune-amplifier.png)
genomic coordinates.](fig6.png.1 "fig6.png")&genomic coordinates.](fig6.png)
out.](images/fig1.png "Fig 1")&out.](fig1.png)
operation.](fig3.png "fig3.png")&operation.](fig3.png)
starts.](images/fig7.png "fig7.png")&starts.](fig7.png)
H).](images/fig7x.png "fig7x.png")&H).](fig7x.png)
](images/fig8.png "fig8.png")*&](fig8.png)*
tumor.](images/fig9.png "fig9.png")**&tumor.](fig9.png)
increases.](fig5.png.1 "fig5.png")&increases.](fig5.png)
scripts/source/replace 0 → 100644
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compute nodes number of workers start-up time[s]&|compute nodes|number of workers|start-up time[s]|
--------------- ------------------- --------------------&|---|---|---|
16 384 831&|16|384|831|
8 192 807&|8|192|807|
4 96 483&|4|96|483|
2 48 16&|2|48|16|
Node type Count Range Memory Cores [Access](resource-allocation-and-job-execution/resources-allocation-policy.html)&|Node type|Count|Range|Memory|Cores|[Access](resource-allocation-and-job-execution/resources-allocation-policy.html)|
---------------------------- ------- --------------- -------- ------------- --------------------------------------------------------------------------------------------------&|---|---|---|---|---|---|
Nodes without accelerator 180 cn[1-180] 64GB 16 @ 2.4Ghz qexp, qprod, qlong, qfree&|Nodes without accelerator|180|cn[1-180]|64GB|16 @ 2.4Ghz|qexp, qprod, qlong, qfree|
Nodes with GPU accelerator 23 cn[181-203] 96GB 16 @ 2.3Ghz qgpu, qprod&|Nodes with GPU accelerator|23|cn[181-203]|96GB|16 @ 2.3Ghz|qgpu, qprod|
Nodes with MIC accelerator 4 cn[204-207] 96GB 16 @ 2.3GHz qmic, qprod&|Nodes with MIC accelerator|4|cn[204-207]|96GB|16 @ 2.3GHz|qmic, qprod|
Fat compute nodes 2 cn[208-209] 512GB 16 @ 2.4GHz qfat, qprod&|Fat compute nodes|2|cn[208-209]|512GB|16 @ 2.4GHz|qfat, qprod|
Node Processor Memory Accelerator&|Node|Processor|Memory|Accelerator|
------------------ --------------------------------------- -------- ----------------------&|---|---|---|---|
w/o accelerator 2x Intel Sandy Bridge E5-2665, 2.4GHz 64GB -&|w/o accelerator|2x Intel Sandy Bridge E5-2665, 2.4GHz|64GB|-|
GPU accelerated 2x Intel Sandy Bridge E5-2470, 2.3GHz 96GB NVIDIA Kepler K20&|GPU accelerated|2x Intel Sandy Bridge E5-2470, 2.3GHz|96GB|NVIDIA Kepler K20|
MIC accelerated 2x Intel Sandy Bridge E5-2470, 2.3GHz 96GB Intel Xeon Phi P5110&|MIC accelerated|2x Intel Sandy Bridge E5-2470, 2.3GHz|96GB|Intel Xeon Phi P5110|
Fat compute node 2x Intel Sandy Bridge E5-2665, 2.4GHz 512GB -&|Fat compute node|2x Intel Sandy Bridge E5-2665, 2.4GHz|512GB|-|
Login address Port Protocol Login node&|Login address|Port|Protocol|Login node|
------------------------ ------ ---------- -----------------------------------------&|---|---|---|---|
salomon.it4i.cz 22 ssh round-robin DNS record for login[1-4]&|salomon.it4i.cz|22|ssh|round-robin DNS record for login[1-4]|
login1.salomon.it4i.cz 22 ssh login1&|login1.salomon.it4i.cz|22|ssh|login1|
login2.salomon.it4i.cz 22 ssh login2&|login1.salomon.it4i.cz|22|ssh|login1|
login3.salomon.it4i.cz 22 ssh login3&|login1.salomon.it4i.cz|22|ssh|login1|
login4.salomon.it4i.cz 22 ssh login4&|login1.salomon.it4i.cz|22|ssh|login1|
Toolchain Module(s)&|Toolchain|Module(s)|
-------------------- ------------------------------------------------&|---|----|
GCC GCC&|GCC|GCC|
ictce icc, ifort, imkl, impi&|ictce|icc, ifort, imkl, impi|
intel GCC, icc, ifort, imkl, impi&|intel|GCC, icc, ifort, imkl, impi|
gompi GCC, OpenMPI&|gompi|GCC, OpenMPI|
goolf BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK&|goolf|BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK|
>iompi OpenMPI, icc, ifort&|iompi|OpenMPI, icc, ifort|
iccifort icc, ifort&|iccifort|icc, ifort|
Login address Port Protocol Login node& |Login address|Port|Protocol|Login node|
------------------------------ ------ ---------- ----------------------------------& |---|---|
salomon-prace.it4i.cz 2222 gsissh login1, login2, login3 or login4& |salomon-prace.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
login1-prace.salomon.it4i.cz 2222 gsissh login1& |login1-prace.salomon.it4i.cz|2222|gsissh|login1|
login2-prace.salomon.it4i.cz 2222 gsissh login2& |login2-prace.salomon.it4i.cz|2222|gsissh|login2|
login3-prace.salomon.it4i.cz 2222 gsissh login3& |login3-prace.salomon.it4i.cz|2222|gsissh|login3|
login4-prace.salomon.it4i.cz 2222 gsissh login4& |login4-prace.salomon.it4i.cz|2222|gsissh|login4|
|Login address|Port|Protocol|Login node|& |Login address|Port|Protocol|Login node|
------------------------ ------ ---------- ----------------------------------& |---|---|
salomon.it4i.cz 2222 gsissh login1, login2, login3 or login4& |salomon.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
login1.salomon.it4i.cz 2222 gsissh login1& |login1.salomon.it4i.cz|2222|gsissh|login1|
login2.salomon.it4i.cz 2222 gsissh login2& |login2-prace.salomon.it4i.cz|2222|gsissh|login2|
login3.salomon.it4i.cz 2222 gsissh login3& |login3-prace.salomon.it4i.cz|2222|gsissh|login3|
login4.salomon.it4i.cz 2222 gsissh login4& |login4-prace.salomon.it4i.cz|2222|gsissh|login4|
Login address Port Node role& |Login address|Port|Node role|
------------------------------- ------ -----------------------------& |---|---|
gridftp-prace.salomon.it4i.cz 2812 Front end /control server& |gridftp-prace.salomon.it4i.cz|2812|Front end /control server|
lgw1-prace.salomon.it4i.cz 2813 Backend / data mover server& |lgw1-prace.salomon.it4i.cz|2813|Backend / data mover server|
lgw2-prace.salomon.it4i.cz 2813 Backend / data mover server& |lgw2-prace.salomon.it4i.cz|2813|Backend / data mover server|
lgw3-prace.salomon.it4i.cz 2813 Backend / data mover server& |lgw3-prace.salomon.it4i.cz|2813|Backend / data mover server|
Login address Port Node role& |Login address|Port|Node role|
------------------------- ------ -----------------------------& |---|---|
gridftp.salomon.it4i.cz 2812 Front end /control server& |gridftp.salomon.it4i.cz|2812|Front end /control server|
lgw1.salomon.it4i.cz 2813 Backend / data mover server& |lgw1.salomon.it4i.cz|2813|Backend / data mover server|
lgw2.salomon.it4i.cz 2813 Backend / data mover server& |lgw2.salomon.it4i.cz|2813|Backend / data mover server|
lgw3.salomon.it4i.cz 2813 Backend / data mover server& |lgw3.salomon.it4i.cz|2813|Backend / data mover server|
File system mount point Filesystem Comment& |File system mount point|Filesystem|Comment|
------------------------- ------------ ----------------------------------------------------------------& |---|---|
/home Lustre Default HOME directories of users in format /home/prace/login/& |/home|Lustre|Default HOME directories of users in format /home/prace/login/|
/scratch Lustre Shared SCRATCH mounted on the whole cluster& |/scratch|Lustre|Shared SCRATCH mounted on the whole cluster|
Data type Default path& |Data type|Default path|
------------------------------ ---------------------------------& |---|---|
large project files /scratch/work/user/prace/login/& |large project files|/scratch/work/user/prace/login/|
large scratch/temporary data /scratch/temp/& |large scratch/temporary data|/scratch/temp/|
---------------------------------------------------------------------------------------------------------------------------------------------&
queue Active project Project resources Nodes priority authorization walltime&|queue|Active project|Project resources|Nodes|priority|authorization|walltime default/max|
default/max&
--------------------- -|---|---|---|--------------------- ---------- --------------- -------------&|---|---|
**qexp** no none required 32 nodes, max 8 per user 150 no 1 / 1h& |**qexp** Express queue|no|none required|32 nodes, max 8 per user|150|no|1 / 1h|
Express queue&\\
**qprace** yes &gt; 0 >1006 nodes, max 86 per job 0 no 24 / 48h&|**qprace** Production queue|yes|&gt; 0|1006 nodes, max 86 per job|0|no|24 / 48h|
Production queue&\\
**qfree** yes none required 752 nodes, max 86 per job -1024 no 12 / 12h&|**qfree** Free resource queue|yes|none required|752 nodes, max 86 per job|-1024|no|12 / 12h|
Free resource queue&\\
---------------------------------------------------------------------------------------------------------------------------------------------&
Port Protocol& |Port|Protocol|
------ ----------& |---|---|
22 ssh& |22|ssh|
80 http& |80|http|
443 https& |443|https|
9418 git& |9418|git|
Node Count Processor Cores Memory Accelerator& |Node|Count|Processor|Cores|Memory|Accelerator|
----------------- ------- ---------------------------------- ------- -------- --------------------------------------------& |---|---|
w/o accelerator 576 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB -& |w/o accelerator|576|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|-|
MIC accelerated 432 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB 2x Intel Xeon Phi 7120P, 61cores, 16GB RAM& |MIC accelerated|432|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|2x Intel Xeon Phi 7120P, 61cores, 16GB RAM|
Node Count Processor Cores Memory GPU Accelerator& |Node|Count|Processor|Cores|Memory|GPU Accelerator|
--------------- ------- --------------------------------- ------- -------- ------------------------------& |---|---|
visualization 2 2x Intel Xeon E5-2695v3, 2.3GHz 28 512GB NVIDIA QUADRO K5000, 4GB RAM& |visualization|2|2x Intel Xeon E5-2695v3, 2.3GHz|28|512GB|NVIDIA QUADRO K5000, 4GB RAM|
Hypercube dimension& |Hypercube|dimension|
--------------------- -------------------------------------------& |---|---|
1D ehc_1d& |1D|ehc_1d|
2D ehc_2d& |2D|ehc_2d|
3D ehc_3d& |3D|ehc_3d|
4D ehc_4d& |4D|ehc_4d|
5D ehc_5d& |5D|ehc_5d|
6D ehc_6d& |6D|ehc_6d|
7D ehc_7d& |7D|ehc_7d|
Node type Count Short name Long name Rack& |Node type|Count|Short name|Long name|Rack|
-------------------------------------- ------- ------------------ -------------------------- -------& |---|---|
M-Cell compute nodes w/o accelerator 576 cns1 -cns576 r1i0n0 - r4i7n17 1-4& |M-Cell compute nodes w/o accelerator|576|cns1 -cns576|r1i0n0 - r4i7n17|1-4|
compute nodes MIC accelerated 432 cns577 - cns1008 r21u01n577 - r37u31n1008 21-38& |compute nodes MIC accelerated|432|cns577 - cns1008|r21u01n577 - r37u31n1008|21-38|
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------&
Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services& |Mountpoint|Usage|Protocol|Net|Capacity|Throughput|Limitations|Access|
---------------------------------------------- -------------------------------- ------------- -------------- ------------ ------------- ------------------------- -----------------------------& |---|---|
/home home directory NFS, 2-Tier 0.5 PB 6 GB/s Quota 250GB Compute and login nodes backed up&| /home|home directory|NFS, 2-Tier|0.5 PB|6 GB/s|Quota 250GB|Compute and login nodes|backed up|
/scratch/work large project files Lustre 1.69 PB 30 GB/s Quota Compute and login nodes none& |/scratch/work|large project files|Lustre|1.69 PB|30 GB/s|Quota|Compute and login nodes|none|
1TB&
/scratch/temp job temporary data Lustre 1.69 PB 30 GB/s Quota 100TB Compute and login nodes files older 90 days removed& |/scratch/temp|job temporary data|Lustre|1.69 PB|30 GB/s|Quota 100TB|Compute and login nodes|files older 90 days removed|
/ramdisk job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends& |/ramdisk|job temporary data, node local|local|120GB|90 GB/s|none|Compute nodes|purged after job ends|
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------&
Application Version module& |Application|Version|module|
------------- -------------- ---------------------& |---|---|
**R** R 3.1.1 R/3.1.1-intel-2015b& |**R**|R 3.1.1|R/3.1.1-intel-2015b|
**Rstudio** Rstudio 0.97 Rstudio& |**Rstudio**|Rstudio 0.97|Rstudio|
24 MPI**&**24 MPI**
--------------- -----------------------& |**Version**|**Module**|
**Version** **Module**& |---|---|
2016 Update 2 Advisor/2016_update2& |2016 Update 2|Advisor/2016_update2|
2016 Update 1 Inspector/2016_update1& |2016 Update 1|Inspector/2016_update1|
Interface Integer type& |Interface|Integer type|
----------- -----------------------------------------------& |---|---|
LP64 32-bit, int, integer(kind=4), MPI_INT& |LP64|32-bit, int, integer(kind=4), MPI_INT|
ILP64 64-bit, long int, integer(kind=8), MPI_INT64 & |ILP64|64-bit, long int, integer(kind=8), MPI_INT64|
Parameter Value& |Parameter|Value|
------------------------------------------------- -----------------------------& |---|---|
>max number of atoms 200& |max number of atoms|200|
>max number of valence orbitals 300& |max number of valence orbitals|300|
>max number of basis functions 4095& |max number of basis functions|4095|
>max number of states per symmmetry 20& |max number of states per symmmetry|20|
>max number of state symmetries 16& |max number of state symmetries|16|
>max number of records 200& |max number of records|200|
>max number of primitives >maxbfn x [2]& |max number of primitives|maxbfn x [2]|
Address Port Protocol& |Address|Port|Protocol|
-------------------------------------------------- ---------------------------------- -----------------------------------------& |---|---|
anselm.it4i.cz 22 scp, sftp& |anselm.it4i.cz|22|scp, sftp|
login1.anselm.it4i.cz 22 scp, sftp& |login1.anselm.it4i.cz|22|scp, sftp|
login2.anselm.it4i.cz 22 scp, sftp& |login2.anselm.it4i.cz|22|scp, sftp|
class="discreet">dm1.anselm.it4i.cz 22 class="discreet">scp, sftp</span>& |dm1.anselm.it4i.cz|22|scp, sftp|
Login address Port Protocol Login node& |Login address|Port|Protocol|Login node|
----------------------- ------ ---------- ----------------------------------------------& |---|----|
anselm.it4i.cz 22 ssh round-robin DNS record for login1 and login2& |anselm.it4i.cz|22|ssh|round-robin DNS record for login1 and login2|
login1.anselm.it4i.cz 22 ssh login1& |login1.anselm.it4i.cz|22|ssh|login1|
login2.anselm.it4i.cz 22 ssh login2& |login2.anselm.it4i.cz|22|ssh|login2|