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calculation_servers

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calculation_servers [2021/06/29 13:28] – created bonnefoncalculation_servers [2023/11/01 20:18] (current) – external edit 127.0.0.1
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-Firstly, img-microgpu1 and img-microgpu2 have retired, too old and obsolete (I'm looking to move the K40 gpu that was in microgpu2 into another server for small tasks).+===== CBI common calculation servers =====
  
-Then, the authentication on the servers has changed, until now we had an LDAP register hosted in the CBI, this is not the case anymore. You can now authenticate yourself on the servers directly using your IGBMC credentials, so the username should be the same, and if you had the same password, it will then be transparent for you.+You can authenticate yourself on the servers directly using your IGBMC credentials, so the username should be the same, and if you had the same password, it will then be transparent for you. 
 + 
 +<quote>ssh <login>@<server_name></quote> 
 + 
 +If you are outside IGBMC you first need to log to a gateway: <quote>ssh -XC <login>@passh.u-strasbg.fr</quote>
  
 Here is the updated name list: Here is the updated name list:
  
-cbi-compute-01 +  * cbi-compute-01 
-cbi-compute-02  +  * cbi-gpu-03 
-cbi-compute-03 +  * cbi-gpu-04 
-cbi-compute-04 + 
-cbi-gpu-03 + 
-cbi-gpu-04+Useful commands 
 +  * check the slurm queue: <quote>squeue</quote> 
 +  * check the GPU usage : <quote>nvidia-smi</quote> 
 +  * check the software available: <quote>module avail</quote> 
 + 
 +---- 
 + 
 +=== Server specifications === 
 + 
 + 
 +**cbi-compute-01** 
 +  * CPU: Intel(R) Xeon(R) CPU E7-4880 v2 @ 2.50GHz 
 +  * Mem: 1 TB 
 + 
 +**cbi-gpu-03** 
 +  * CPU: Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz *2 
 +  * Mem: 128 GB 
 +  * GPU: GK210GL [Tesla K80] 12 GB *4 
 + 
 +**cbi-gpu-04** 
 +  * CPU: Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz *2 
 +  * Mem: 128 GB 
 +  * GPU: GK210GL [Tesla K80] 12 GB *2 
 +  * GPU: GP100GL [Tesla P100 PCIe 16GB] 
 + 
 + 
 +---- 
 + 
 +=== Available softwares === 
 + 
 +as of 2023-05-11 
 + 
 +**cbi-compute-01** 
 +  * <quote>/usr/local/modules/modulefiles</quote> 
 +<code> 
 +autoproc/2018  ccpem/1.4.1-nightly  gamess/20170511  phenix/1.11.1  relion/3.1.2-cpu   
 +buster/2016    cistem/1.0.0-beta    imagic/170515    phenix/1.12    xds/2017-03-02     
 +buster/2017    dynamo/1.1.291        imagic/181101    phenix/1.14    xds/2017-06-12     
 +buster/2018  eman2/2.3    imod/4.8.14    phenix/1.18  xds/2018-04-03   
 +ccp4/7.0      eman2/2.9    imod/4.9.5      phenix/1.19  xdsme/20170529 
 +ccpem/1.0.0  eman2/2.31  modeller/9.20  rave/2008    xmipp/3.19 
 +</code> 
 +  * <quote>/opt/CBI/modulefiles</quote> 
 +<code> 
 +phenix/1.13-2998  relion/2.0.3-cpu  relion/2.1-cpu 
 +</code> 
 +  * <quote>/mnt/storage/software/modulefiles</quote> 
 +<code> 
 +4.0.0-stable        cistem/1.0          dynamo/1.1.514  motioncor2/1.5.0  relion/4.0.0    
 +itom/2022-03-10     cistem/2021-05-03  eman2/2.9        motioncor2/1.6.3  resmap/1.95     
 +utoproc/2021-04-20  cryodrgn/0.3.4      imod/4.11.5      phenix/1.19.2      rosetta/3.13 
 +uster/2021-04-20    cryolo-cpu/1.7      imod/4.11.8      pyem/0.5          scipion/3.0.0 
 +ccp4/7.1          cryolo-gpu/1.7          imosflm/7.4.0        pymol/2.5.0         topaz/0.2.5 
 +ccpem/1.5.0        cryolo-gpu/1.8          microed_tools/0.1.0 pyrosetta/291       xds/2021-02-05 
 +chimera/1.15      ctffind/4.1.14          modeller/10.2        relion/3.1.2             
 +chimeraX/1.2      deep-finder/2021-04-15  motioncor2/1.4.2    relion/3.1.3(default)   
 + 
 +</code> 
 + 
 +**cbi-gpu-03** 
 +  * <quote>/usr/local/modules/modulefiles</quote> 
 +<code> 
 +chimera/1.11.2  cryolo/1.7  dynamo/1.1.291  eman2/2.2  eman2/2.3  eman2/2.9  eman2/2.12   
 +imod/4.8.14     imod/4.9.5  imod/4.9.12  motioncor2/1.4  relion/3.1.2-gpu  topaz/0.2.4 
 +</code> 
 +  * <quote>/opt/CBI/modulefiles</quote> 
 +<code> 
 +relion/2.0.3-gpu  relion/2.1-gpu 
 +</code> 
 +  * <quote>/mnt/storage/software/modulefiles</quote> 
 +<code> 
 +4.0.0-stable          cistem/1.0          dynamo/1.1.514  motioncor2/1.5.0  relion/4.0.0    
 +aitom/2022-03-10      cistem/2021-05-03  eman2/2.9        motioncor2/1.6.3  resmap/1.95     
 +autoproc/2021-04-20  cryodrgn/0.3.4      imod/4.11.5      phenix/1.19.2      rosetta/3.13 
 +buster/2021-04-20    cryolo-cpu/1.7      imod/4.11.8      pyem/0.5          scipion/3.0.0 
 +ccp4/7.1              cryolo-gpu/1.7          imosflm/7.4.0        pymol/2.5.0            topaz/0.2.5 
 +ccpem/1.5.0            cryolo-gpu/1.8          microed_tools/0.1.0  pyrosetta/291          xds/2021-02-05 
 +chimera/1.15          ctffind/4.1.14          modeller/10.2        relion/3.1.2             
 +chimeraX/1.2          deep-finder/2021-04-15  motioncor2/1.4.2      relion/3.1.3(default) 
 +</code> 
 + 
 +**cbi-gpu-04** 
 +  * <quote>/mnt/storage/software/modulefiles</quote> 
 +<code> 
 +4.0.0-stable cistem/1.0             dynamo/1.1.514          motioncor2/1.5.0  relion/4.0.0    
 +aitom/2022-03-10 cistem/2021-05-03      eman2/2.9                motioncor2/1.6.3  resmap/1.95     
 +autoproc/2021-04-20 cryodrgn/0.3.4         imod/4.11.5              phenix/1.19.2      rosetta/3.13 
 +buster/2021-04-20 cryolo-cpu/1.7         imod/4.11.8              pyem/0.5          scipion/3.0.0 
 +ccp4/7.1      cryolo-gpu/1.7        imosflm/7.4.0 pymol/2.5.0 topaz/0.2.5 
 +ccpem/1.5.0    cryolo-gpu/1.8        microed_tools/0.1.0 pyrosetta/291 xds/2021-02-05 
 +chimera/1.15  ctffind/4.1.14        modeller/10.2 relion/3.1.2             
 +chimeraX/1.2  deep-finder/2021-04-15 motioncor2/1.4.2         relion/3.1.3(default) 
 +</code>
  
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