Maestro – Schrodinger <2019

2020(e)ko uztailaren 28a

Quick Guide of Maestro: https://www.schrodinger.com/sites/default/files/maestro_qrc_18_0.pdf

Licencia y Variables de entorno :  /etc/profile.d/schrodinger.sh

export SCHROD_LICENSE_FILE=29007@lic-schrodinger-231.ehu.es
export SCHRODINGER=/software/schrodinger
export SCHRODINGER_TEMP_PROJECT=/scratch/$USER/.schrodinger
export PATH=/software/schrodinger:$PATH

Katramila: 2020.07.28

Running maestro give an error on the license file and automatically started with a license setup:

/software/schrodinger/mmshare-v4.6/bin/Linux-x86_64/lmutil lmdiag -n -c 29007@lic-schrodinger-231.ehu.es

An error has occurred. Information about the error has been written to
/home/qjornet/.schrodinger/exceptions/error20200728-115749.txt (falta de permisos, lo estaba haciendo como qjornet)

 

Probando /software/schrodinger/licadmin :

 

Kalk2017:

Sailkatugabeak

Multiples Nodos xeon20 Down !

2020(e)ko uztailaren 21a

2020.07.21

DOWN = nb7
DOWN = nb13
DOWN = nb32

– Ninguno responde al ping (salvo nb32).

– Intento entrar en consola por ipmitool.

DOWN = nb32
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
——————– ——– ——– —————- —— —– — —— —– – —–
59476.arina quamearx p_sslow base4serie1 25361 1 — 100gb 300:0 E 300:2 nb32/2
68175.arina enxgabua n_short Li30Ti3Ge1S16S6I 366 1 — — 23:58 R 08:27 nb32/0
51627.arina qovzaxxr p_sslow l_09 32467 1 — 4gb 599:0 R 368:0 nb32/19+nb32/18+nb32/17+nb32/16

[qjornet@nb0 ~]$ ssh nb32
ssh_exchange_identification: Connection closed by remote host
[root@nb0 qjornet]# ssh nb32
Last login: Fri Jun 5 16:34:12 2020
(staked)…

Sigo instrucciones entrada: nb9 down – GATEWAY error

a) pbsnodes -o nb32
b) gama0# conman n32  –> se queda intentando acceder a la shell, como le pasa a ssh.
c) clmctrl status n32
WARNING – n32: ERROR: Command failed.
n32: ERROR: Address lookup for bmc32 failed
n32: ERROR: opening interface lan
ERROR – n32: [rc=1] ERROR: Command failed.
d) He entrado por firefox / 10.128.31.133 (bmc32) / Katramila passwd BMC –
Veo en Server Health/Event Log:

108 2020/06/15 22:31:39 OEM Memory Correctable Memory ECC @ DIMMD1(CPU1)
e) Trying “Maintenance / Unit Reset” –> nada se queda bloqueado en:
[root@gama0 ~]# shine status
[09:52] In progress for 10 component(s) on 10 servers …
[09:53] In progress for 1 component(s) on n32 …

f) en Remote Control : Power Off Server – Orderly Shutdown
Performing soft power off failed. This may be because the host OS is taking an unusually long time to gracefully shut down. If you think this is not the case please check The feature connector cables.

g) en Remote Control : Power Off Server – Immediatly
Remote Control : Power On Server
(paraver el estado de la reinicialización se puede hacer un “Refresh Preview Image” en System.
Ya se conecta con ssh !

h) Montar gscratch !
root@nb32 ]# hostname n32
[root@mama0 ~]# shine mount -f gscratch -n n32
[root@nb0 qjornet]# ssh nb32

i) pbsnodes -c nb32

OK !!!

 

Sailkatugabeak

GROMACS 2020 – fosscuda

2020(e)ko ekainaren 3a

La instalación se ha hecho con Easybuild, y el easyconfig de :

/home/qjornet/SOFTWARE/srcs/EasyBuild/easyconfigs_qjs/software/g/GROMACS/GROMACS-2020-fosscuda-2018b.eb

 

nd15-

Tiene salida exterior – se ha instalado los paquetes con yum:  yum install libibverbs-devel

nb32

  1. en katramila: instalamos:    eb CMake-3.11.4-GCCcore-7.3.0.eb -r
  2. en katramila –fetch software: [qjornet@nb0 GROMACS]$ eb GROMACS-2020-fosscuda-2018b.eb -r –fetch

instalar packages as root: en katramila :

yumdownloader –resolve –destdir=/software/SETUP/GROMACS/openssl-devel openssl-devel
yumdownloader –resolve –destdir=/software/SETUP/GROMACS/libibverbs-devel libibverbs-devel

y otros….com libverto-devel, keyutils-libs-devel, libcom_err-devel,  libselinux-devel.

ssh nb32 ->

[root@nb32 openssl-devel-test]# ls -lrrt
total 2644
-rw-r–r–. 1 root root 38280 Apr 1 2014 keyutils-libs-devel-1.5.8-3.el7.x86_64.rpm
-rw-r–r–. 1 root root 72348 Apr 2 2014 libsepol-devel-2.1.9-3.el7.x86_64.rpm
-rw-r–r–. 1 root root 11828 Apr 2 2014 libverto-devel-0.2.5-4.el7.x86_64.rpm
-rw-r–r–. 1 root root 178588 Apr 9 2014 libselinux-devel-2.2.2-6.el7.x86_64.rpm
-rw-r–r–. 1 root root 1235740 Jun 26 2015 openssl-devel-1.0.1e-42.el7_1.9.x86_64.rpm
-rw-r–r–. 1 root root 428280 Oct 5 2015 pcre-8.32-15.el7.x86_64.rpm
-rw-r–r–. 1 root root 664880 Oct 14 2015 krb5-devel-1.13.2-10.el7.x86_64.rpm
-rw-r–r–. 1 root root 30580 Nov 8 2016 libcom_err-devel-1.42.13.wc5-7.el7.x86_64.rpm

[root@nb32 libibverbs-devel]# rpm -ihfv  *

Update openssl to 1.0.2 (CMAKE requires openssl 1.0.2 or higher)

[root@nb32 openssl-1.0.2]# ls -lrt

-rw-r–r–. 1 root root 1248228 Jun  4 19:57 openssl-libs-1.0.2k-8.el7.x86_64.rpm
-rw-r–r–. 1 root root 1578824 Jun  4 19:57 openssl-devel-1.0.2k-8.el7.x86_64.rpm
-rw-r–r–. 1 root root  503440 Jun  4 19:57 openssl-1.0.2k-8.el7.x86_64.rpm

[root@nb32 openssl-1.0.2]# rpm -Uhfv *                                           

[qjornet@nb32 GROMACS]$ eb GROMACS-2020-fosscuda-2018b.eb -r

 

NEW FORCE FIELDS : Gabriele Dalla Torre asked me to put them on $EBROOTGROMACS/share/gromacs/top

he charmm36.ff folder contains the charmm36m force field, which is designed for disordered proteins:
This force field was downloaded form the author’s website:
The a99disp.ff folder contains the a99SB-disp force field, which is designed for disordered proteins:
The two DES-amber.ff folders contains two versions of the DES-amber force field (more on that below) which are designed for protein-protein interactions:
The three amber force fields above were downloaded form the author’s github repository:
Importantly, if someone is planning to use on of the three amber force field mentioned above, she/he shold be aware of the following things (taken from the DISCLAIMER file included in the .tar archive)

#######Please Cite: ###########

Water dispersion interactions strongly influence simulated structural properties of disordered protein states
S Piana, AG Donchev, P Robustelli, DE Shaw
The journal of physical chemistry B 119 (16), 5113-5123

Developing a molecular dynamics force field for both folded and disordered protein states
P Robustelli, S Piana, DE Shaw
Proceedings of the National Academy of Sciences 115 (21), E4758-E4766

Development of a force field for the simulation of single-chain proteins and protein-protein complexes
S Piana, P Robustelli, D Tan, S Chen, DE Shaw
Journal of Chemical Theory and Computation

###############################

a99SB-disp is intended for use with the a99SBdisp water model and c22 ions.

DES-amber and DES-amberSF1.10 parameres are intended for use with the TIP4P-D water model, and contain their own ion parameters

The Gromacs versions were adopted from DESMOND viparr parameters.

Please note that all published simulations were performed using a DESMOND version of the force-fields.

GROMACS versions were created for the convenience of external researchers.

Basic tests have indicated that the GROMACS versions should provide accurate parameters that correctly reproduce the DESMOND force-field, but we cannot cannot guarantee that they are free from any bug.

To ensure accuracy for your system, you should compare FF energies to energies obtained from DESMOND using official viparr-ff releease.

##############################

######  a99SB-disp Notes #####
The gromacs implementation of a99SBdisp.ff contians parameters for c22ions and a99SBdisp water

These parameters can be compared against
Desmond/a99SBdisp_viparr-ff/
aa.amber.ff99SB-disp  ions.charmm22  water.tip4pd-1.6

These a99SBdisp parameters were taken from the public viparr-ff repository
https://github.com/DEShawResearch/viparr-ffpublic

##### DES-amber Notes   ######
The gromacs implementations of des-amber.ff and des-amber-SF1.0.ff contain their own ion parameters and tip4p-D wtaer parameters and can be compared to:

Robustelli_Lab_ForceFields/Desmond
des-amber  des-amber-SF1.0  water.tip4pd

These viparr implementations are *not* official D.E. Shaw Research releases, and should be considered personal implementations.  D.E. Shaw Research should be contacted about official DES-amber viparr force field releases.

##### Note on DES-amber Charge Scaling ######

DES-amber has charges an ions that are scaled by a factor of 0.9

This means if you are combining this force fields with lipids, ligands, or nucleic acids
with net  charges, the total charge of the system will not be equal

You can either scale the charges of the other molecules (not recommended )
or use DES-amber_SF1.0 (scale factor 1.0) which does not contain scaled charges

Sailkatugabeak

nb7 “general protection fault: 0000 [#1] SMP” “RIP __schedule”

2019(e)ko azaroaren 25a

nb7 estando en Offline, llena /boot/var/crash/127.0.0.1-2019-11-14-15:53:58   con 500MB.

Según link : https://stackoverflow.com/questions/20867933/linux-kernel-module-crash-debug-general-protection-fault-0000-1-smp

(https://opensourceforu.com/2011/01/understanding-a-kernel-oops/)

 

[945500.393511] =========== Date: Thu Nov 14 15:00:01 CET 2019 ===============
[945559.919772] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[945680.044585] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[945860.669350] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[946040.293503] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[946220.929331] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[946400.598962] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[946580.748718] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[946760.881314] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[946918.309918] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[946941.193359] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[947120.912235] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[947301.230045] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[947481.558580] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[947661.886645] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[947773.650582] epilogue (17409): drop_caches: 3
[947841.224998] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[948021.591313] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[948201.898937] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[948382.198736] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[948562.505236] SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs
[948725.728516] general protection fault: 0000 [#1] SMP
[948725.733608] Modules linked in: osc(OE) mgc(OE) lustre(OE) lmv(OE) fld(OE) mdc(OE) fid(OE) lov(OE) ko2iblnd(OE) ptlrpc(OE) obdclass(OE) lnet(OE) sha512_generic crypto_null libcfs(OE) ipmi_devintf nfsv3 rpcsec_gss_krb5 fuse nfsv4 dns_resolver nfs fscache rdma_ucm(OE) ib_ucm(OE) rdma_cm(OE) iw_cm(OE) ib_ipoib(OE) ib_cm(OE) ib_uverbs(OE) ib_umad(OE) mlx5_ib(OE) mlx5_core(OE) mlx4_en(OE) vxlan ip6_udp_tunnel udp_tunnel intel_powerclamp coretemp kvm_intel kvm iTCO_wdt iTCO_vendor_support crc32_pclmul ghash_clmulni_intel aesni_intel lrw gf128mul glue_helper ablk_helper cryptd mgag200 syscopyarea sysfillrect sysimgblt ttm drm_kms_helper mei_me drm mei lpc_ich sg pcspkr mfd_core shpchp ioatdma i2c_i801 ipmi_si wmi ipmi_msghandler acpi_pad nfsd auth_rpcgss nfs_acl lockd grace sunrpc ip_tables ext4 mbcache
[948725.805264] jbd2 mlx4_ib(OE) ib_sa(OE) ib_mad(OE) ib_core(OE) ib_addr(OE) ib_netlink(OE) sd_mod crc_t10dif crct10dif_generic igb isci ptp libsas pps_core ahci i2c_algo_bit libahci scsi_transport_sas i2c_core crct10dif_pclmul crct10dif_common mlx4_core(OE) libata dca crc32c_intel mlx_compat(OE) dm_mirror dm_region_hash dm_log dm_mod
[948725.833932] CPU: 5 PID: 15752 Comm: l502.exel Tainted: G OE ———— 3.10.0-327.36.1.el7.x86_64 #1
[948725.844450] Hardware name: BULL bullx blade/SCBF, BIOS BIOSX03.040.04.204 07/30/2015.11:05:28
[948725.853055] task: ffff88102488f300 ti: ffff880faea50000 task.ti: ffff880faea50000
[948725.860624] RIP: 0010:[<ffffffff8163b1a5>] [<ffffffff8163b1a5>] __schedule+0xc5/0x900
[948725.868648] RSP: 0018:ffff880faea53f10 EFLAGS: 00010046
[948725.874051] RAX: 3e84a0cdd7eae2a1 RBX: ffff88102488f8e8 RCX: ffff88102488f300
[948725.881266] RDX: 00000000000018ca RSI: ffff8810ffff8810 RDI: ffff88103ef567c0
[948725.888483] RBP: ffff880faea53f60 R08: 00000000004db6d0 R09: 00000000000000b0
[948725.895698] R10: 0000000000021000 R11: 0000000000000286 R12: ffff88103ef567c0
[948725.902915] R13: 0000000000000005 R14: 00007ffd60a4d658 R15: 0000000000000041
[948725.910130] FS: 00002ba14b5ad700(0000) GS:ffff88103ef40000(0000) knlGS:0000000000000000
[948725.918300] CS: 0010 DS: 0000 ES: 0000 CR0: 0000000080050033
[948725.924129] CR2: 000000005cc7ba2c CR3: 00000010251e2000 CR4: 00000000001407e0
[948725.931346] DR0: 0000000000000000 DR1: 0000000000000000 DR2: 0000000000000000
[948725.938561] DR3: 0000000000000000 DR6: 00000000ffff0ff0 DR7: 0000000000000400
[948725.945778] Stack:
[948725.947876] ffff88102488f300 ffff880faea53fd8 ffff880faea53fd8 ffff880faea53fd8
[948725.955421] ffff88102488f300 ffff88103ef567c0 0000000000000008 00007ffd00007ffd
[948725.962968] 00007ffd60a4d658 0000000000000041 ffff880faea53f78 ffffffff810b7fd5
[948725.970512] Call Trace:
[948725.973051] [<ffffffff810b7fd5>] sys_sched_yield+0x65/0xd0
[948725.978713] [<ffffffff81646a09>] system_call_fastpath+0x16/0x1b
[948725.984807] Code: 8b 45 d0 48 8d 98 e8 05 00 00 48 8b 00 48 85 c0 74 11 48 8b 45 b8 f6 80 47 c0 ff ff 10 0f 84 93 04 00 00 48 8b 75 d0 48 8b 46 60 <48> 8b 40 50 48 85 c0 74 05 4c 89 e7 ff d0 45 8b 5c 24 04 45 85
[948726.004857] RIP [<ffffffff8163b1a5>] __schedule+0xc5/0x900
[948726.010530] RSP <ffff880faea53f10>

Inzidentziak, nb7, Sailkatugabeak

SqueezeMeta

2019(e)ko azaroaren 20a

Installation instructions from

PAQUETES QUE FALTAN EN NODOS: ( /software/SETUP/SQUEEZEMETA )

### Enable Extended Packages for Enterprise Linux.
sudo yum -y install epel-release

### Install git and system libraries
sudo yum -y install ncurses-devel -(installed ncurses-devel-5.9-13.20130511.el7.x86_64.rpm)
git
zlib-devel  — already installed  1.2.7-15.el7
bzip2-devel — ” 1.0.6-13.el7
xz-devel  —– DOWNLOADED: 5.1.2-12alpha.el7 (according to already installed xz-libs)

### Install Ruby.
sudo yum -y install ruby  —- already installed 2.0.0.598-25.el7_1

### Install Perl modules.
sudo yum -y install cpan  — installed against perl 5.16.3 (arleady installed)
perl-Tie-IxHash   — installed perl-Tie-IxHash-1.22-11.el7.noarch.rpm
perl-DBI
perl-DBD-mysql
perl-XML-LibXML
perl-XML-Parser
perl-DBD-SQLite
perl-Time-Piece    —– DOWNLOADED

sudo cpan DBD::SQLite::Constants

###Install Python modules.
sudo yum -y install python3 python36-scipy

Lo hacemos correr sobre ANACONDA /software/anaconda3  (export PATH=”/software/anaconda3/bin/:$PATH”)
conda install -c bioconda dendropy  — DONE
conda install -c bioconda pysam   — DONE

sudo python3 -m pip install matplotlib dendropy pysam

### Install R.
installed with anaconda:
ya está en el PATH : con anaconda 3.5.1 !!! en software/bin/R es 3.3.3
sudo yum -y install R

### Download SqueezeMeta.
## You can download the latest release of SqueezeMeta from https://github.com/jtamames/SqueezeM/releases/latest
## Alternatively you can clone the github repository.
## git clone http://github.com/jtamames/SqueezeMeta

### Install R packages.
sudo R
install.packages(“doMC”)  — OK
install.packages(“ggplot2”) — OK
install.packages(“data.table”) — OK
install.packages(“reshape2”)  —  OK
install.packages(“BiocManager”)  — OK
BiocManager::install(“pathview”)  — OK?
quit(save=”no”)
sudo R CMD INSTALL <installpath>/SqueezeMeta/bin/DAS_Tool/package/DASTool_1.1.1.tar.gz  — OK
sudo R CMD INSTALL <installpath>/SqueezeMeta/lib/SQMtools — OK

### Install databases and test data.   ( guardado en /gscratch/SqueezeMeta_DB )
# This will occupy around 200Gb.
<installpath>/SqueezeMeta/scripts/preparing_databases/download_databases.pl <datapath>

### Run SqueezeMeta on test data.
cd <datapath>/test
perl <installpath>/SqueezeMeta/scripts/SqueezeMeta.pl -m merged -p Hadza -s test.samples -f raw/

Sailkatugabeak

IZO/SGI Lan gauzak

2012(e)ko maiatzaren 8a

Blog hau IZO/SGI Sgikeren lan goraberei buruzkoa da. Nagusiki, pribatua mantenduko da. Serbitzuari buruzko informazio gehiago nahi izanez gero begiratu:

 

Zerbitzuko Blog-a:

http://www.ehu.es/ehusfera/hpc

Zerbitzuko Web orria:

http://www.ehu.es/sgi

General Info