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Allocating more GPU chunks for a GPU Nodes in PBS Professional

Check for the Visualisation Node configuration

# qmgr -c " p n VizSvr1"

1. At the Node Configuration at PBS-Professional, the GPU Chunk (“ngpus”) is 10.

#
# Create nodes and set their properties.
#
#
# Create and define node VizSvr1
#
create node VizSvr1
set node VizSvr1 state = free
set node VizSvr1 resources_available.allows_container = False
set node VizSvr1 resources_available.arch = linux
set node VizSvr1 resources_available.host = VizSvr1
set node VizSvr1 resources_available.mem = 791887872kb
set node VizSvr1 resources_available.ncpus = 24
set node VizSvr1 resources_available.ngpus = 10
set node VizSvr1 resources_available.vnode = VizSvr1
set node VizSvr1 queue = iworkq
set node VizSvr1 resv_enable = True

2. At the Queue Level, notice that the gpu chunk (“ngpus”) is 10 and cpu-chunk is 2

[root@scheduler1 ~]# qmgr
Max open servers: 49
Qmgr: p q iworkq
#
# Create queues and set their attributes.
#
#
# Create and define queue iworkq
#
create queue iworkq
set queue iworkq queue_type = Execution
set queue iworkq Priority = 150
set queue iworkq resources_max.ngpus = 10
set queue iworkq resources_min.ngpus = 1
set queue iworkq resources_default.arch = linux
set queue iworkq resources_default.place = free
set queue iworkq default_chunk.mem = 512mb
set queue iworkq default_chunk.ncpus = 2
set queue iworkq enabled = True
set queue iworkq started = True

2a. Configure at the Queue Level: Increase More GPU Chunk so that more users can use. Similarly, lower the CPU Chunk to spread our among the con-current session

Qmgr: set queue iworkq resources_max.ngpus = 20
Qmgr: set queue iworkq default_chunk.ncpus = 1
Qmgr: p q iworkq

2b. Configure at the Node Level: Increase the GPU Chunk at the node level to the number you use at the Queue Level. Make sure the number is the same.

Qmgr: p n hpc-r001
#
# Create nodes and set their properties.
#
#
# Create and define node VizSvr1
#
create node VizSvr1
set node VizSvr1 state = free
set node VizSvr1 resources_available.allows_container = False
set node VizSvr1 resources_available.arch = linux
set node VizSvr1 resources_available.host = VizSvr1
set node VizSvr1 resources_available.mem = 791887872kb
set node VizSvr1 resources_available.ncpus = 24
set node VizSvr1 resources_available.ngpus = 10
set node VizSvr1 resources_available.vnode = VizSvr1
set node VizSvr1 queue = iworkq
set node VizSvr1 resv_enable = True
Qmgr: set node hpc-r001 resources_available.ngpus = 20
Qmgr: q

Can verify by logging more session and testing it

[root@VizSvr1 ~]# qstat -ans | grep iworkq
94544.VizSvr1 user1 iworkq xterm 268906 1 1 256mb 720:0 R 409:5
116984.VizSvr1 user1 iworkq Abaqus 101260 1 1 256mb 720:0 R 76:38
118478.VizSvr1 user2 iworkq Ansys 236421 1 1 256mb 720:0 R 51:37
118487.VizSvr1 user3 iworkq Ansys 255657 1 1 256mb 720:0 R 49:51
119676.VizSvr1 user4 iworkq Ansys 308767 1 1 256mb 720:0 R 41:40
119862.VizSvr1 user5 iworkq Matlab 429798 1 1 256mb 720:0 R 23:54
120949.VizSvr1 user6 iworkq Ansys 450449 1 1 256mb 720:0 R 21:12
121229.VizSvr1 user7 iworkq xterm 85917 1 1 256mb 720:0 R 03:54
121646.VizSvr1 user8 iworkq xterm 101901 1 1 256mb 720:0 R 01:57
121664.VizSvr1 user9 iworkq xterm 111567 1 1 256mb 720:0 R 00:01
121666.VizSvr1 user9 iworkq xterm 112374 1 1 256mb 720:0 R 00:00
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Compiling Quantum ESPRESSO-6.5.0 with Intel MPI 2018 on CentOS 7

Step 1: Download Quantum ESPRESSO 6.5.0 from Quantum ESPRESSO Download Site or git-clone QE

% git clone https://gitlab.com/QEF/q-e.git

Step 2: Remember to source the Intel Compilers and indicate MKLROOT in your .bashrc

source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64
source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64
source /usr/local/intel/2018u3/compilers_and_libraries/linux/bin/compilervars.sh intel64
source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64

Step 3: Make a file call setup.sh and copy the contents inside.

export F90=mpiifort
export F77=mpiifort
export MPIF90=mpiifort
export CC=mpiicc
export CPP="icc -E"
export CFLAGS=$FCFLAGS
export AR=xiar
export BLAS_LIBS=""
export LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64"
export SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64"
export FFT_LIBS="-L$MKLROOT/intel64"
./configure --enable-parallel --enable-openmp --enable-shared --with-scalapack=intel --prefix=/usr/local/espresso-6.5.0
% ./setup.sh
% make all -j 16 
% make install

Checking of availabilities of Libraries

% ./configure --prefix=/usr/local/espresso-6.5.0 --enable-parallel --enable-openmp --enable-shared --with-scalapack=intel | tee Configure.out

Checking Configure.Out, there are some missing libraries which you have to fix.

.....
.....

ESPRESSO can take advantage of several optimized numerical libraries
(essl, fftw, mkl...). This configure script attempts to find them,
but may fail if they have been installed in non-standard locations.
If a required library is not found, the local copy will be compiled.

The following libraries have been found:
BLAS_LIBS= -lblas
LAPACK_LIBS=-L/usr/local/lib -llapack -lblas
FFT_LIBS=
.....
.....

References:

  1. Project Site (https://github.com/QEF/q-e/releases)
  2. Compiling Quantum Espresso
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Installing the Seurat Package on R-3.6.2

Step 1: Compiling R on CentOS 7

a. Download R Package from https://cran.r-project.org/

b. Untar and Compile the R-Package

$ tar -zxvf R-3.6.2.tar.gz
$ cd R-3.6.2
$ ./configure --prefix=/home/myuser/R-3.6.2
$ make
$ make install

Step 2: Compile multtest package
Seurat is dependent on mulltest. But if you try installing muttest using R, you will have this error.

$ cd /home/myuser/R-3.6.2
$ ./R
install.packages("multtest")
Warning message:
package ‘multtest’ is not available (for R version 3.6.2)

To solve the issue, you have to install BiocManager first and use BiocManager to install mulltest

install.packages("BiocManager")
BiocManager::install("multtest")

Step 3: Finally, you can install Seurat

install.packages("Seurat")

References:

    1. Resampling-based multiple hypothesis testing

 

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Fixing Dependencies Resolution on CentOS 7

Taken from RedHat Solutions- “Yum update or yum install fails with package conflict between 64 bit and 32 bit package architectures ?”

You can configure the yum client to update only a package of the exact architecture installed on the system.

[root@node1 R-3.6.2]# yum install libcurl-devel
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
* centos-sclo-rh: mirror.0x.sg
Resolving Dependencies
--> Running transaction check
---> Package libcurl-devel.x86_64 0:7.29.0-42.el7 will be installed
--> Processing Dependency: libcurl = 7.29.0-42.el7 for package: libcurl-devel-7.29.0-42.el7.x86_64
--> Finished Dependency Resolution
Error: Package: libcurl-devel-7.29.0-42.el7.x86_64 (centos74-dvd)
Requires: libcurl = 7.29.0-42.el7
Installed: libcurl-7.29.0-46.el7.x86_64 (installed)
libcurl = 7.29.0-46.el7
Available: libcurl-7.29.0-42.el7.x86_64 (centos74-dvd)
libcurl = 7.29.0-42.el7
You could try using --skip-broken to work around the problem
** Found 139 pre-existing rpmdb problem(s), 'yum check' output follows:

 

You can configure the yum client to update only a package of the exact architecture installed on the system.

1. Install the yum-utils package

yum install yum-utils

2. The package-cleanup –dupes lists all duplicate packages:

# package-cleanup --dupes

3. The package-cleanup –cleandupes removes the duplicates

# package-cleanup --cleandupes

4. Edit /etc/yum.conf, set the following line for CentOS 7:

exactarchlist=*

Run yum command:

# yum clean all
# yum update

References:

  1. “Yum update or yum install fails with package conflict between 64 bit and 32 bit package architectures ?”
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Compiling tesseract-5.0 on CentOS 7

Step 1: Installing the basic CentOS Dependencies

# yum install autoconf automake libtool pkgconfig.x86_64 libpng12-devel.x86_64 libjpeg-devel libtiff-devel.x86_64 zlib-devel.x86_64

Step 2: Compile Leptonica-1.79

Step 3: Compile tesseract-5.0

Load a recent version of GNU C++. In my case, I’ve used GNU-6.5 and ISL-0.18 (Integer Set Library)

a. Yum install git

$ yum install git

b. Configure lept.pc for Leptonica-1.79 if you have placed leptonica in a unique directory

$ export PKG_CONFIG_PATH=/usr/local/leptonica-1.79.0/lib/pkgconfig

c. Compile the Tesseract

$ git clone https://github.com/tesseract-ocr/tesseract.git
$ cd tesseract
$ ./autogen.sh
$ ./configure --prefix=/usr/local/tesseract-5.0 
$ make
$ make install

References:

  1. Using Tesseract on Ubuntu
  2. Tessaract by Ivanzz
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Implementing Docker Group using Centrify

Why Privilege Access For Docker Container?

Taken from Centrify HOWTO: Secure container/docker environments by managing privileges for admins and users

“To perform any docker operation, you need to either be root or part of a local group, ‘docker’, on your Linux machine. Why is that? Because access into a docker container is via a UNIX socket and any socket related operations require the user to have privileged access. ‘Docker’ group membership is sufficient for all container operations, exception is starting the docker daemon itself, which must always run as the root user.”

Step 1:

We need to create a group called Docker and put in the necessary members

Step 2: Verify the permission of the Linux Server

# ls -lZ /var/run/docker.sock
srw-rw----. root root system_u:object_r:container_var_run_t:s0 /var/run/docker.sock
# getenforce
Permissive

Step 3: Change Owner of the Docker

# chown root:docker /var/run/docker.sock

Step 4: Test the change permission issues

[user1@node1 ~]$ docker search openfoam
INDEX NAME DESCRIPTION STARS OFFICIAL AUTOMATED
docker.io docker.io/openfoamplus/of_v30plus_rhel66 Offical image of OpenFOAM+ (v3.0+) provide... 8
docker.io docker.io/openfoamplus/of_v1606plus_centos66 Offical image of OpenFOAM+ (v1606+) provid... 6
docker.io docker.io/openfoam/openfoam5-paraview54 Image of OpenFOAM v5 and ParaView 5.4.0 on... 5
docker.io docker.io/openfoam/openfoam6-paraview56 Image of OpenFOAM v6 and ParaView 5.6.0 on... 5
docker.io docker.io/openfoamplus/of_v1612plus_centos66 Offical image of OpenFOAM+ (v1612+) provid... 5
docker.io docker.io/openfoam/openfoam7-paraview56 Image of OpenFOAM v7 and ParaView 5.6.0 on... 4
docker.io docker.io/openfoamplus/of_v1706_centos73 Offical image of OpenFOAM(v1706) provided ... 4
docker.io docker.io/openfoamplus/of_v1712_centos73 Offical docker image of OpenFOAM(v1712) pr... 4
docker.io docker.io/openfoam/openfoam6-paraview54 Image of OpenFOAM v6 and ParaView 5.4.0 on... 3
docker.io docker.io/openfoamplus/of_v1812_centos73 Offical docker image of OpenFOAM(v1806) pr... 3
docker.io docker.io/openfoamplus/of_v1806_centos73 Offical docker image of OpenFOAM(v1806) pr... 2
docker.io docker.io/openfoamplus/of_v1906_centos73 Official docker image of OpenFOAM(v1906 ve... 2
docker.io docker.io/dicehub/openfoam OpenFOAM image for use in DICE (Dynamic In... 1
docker.io docker.io/openfoam/openfoam-dev-graphical-apps OpenFOAM-dev on Ubuntu 16.04 using the ope... 1
docker.io docker.io/openfoam/openfoam-dev-paraview54 OpenFOAM-dev and ParaView 5.4.0 on Ubuntu ... 1
docker.io docker.io/openfoam/openfoam-dev-paraview56 Image of OpenFOAM-dev and ParaView 5.6.0 o... 1
docker.io docker.io/openfoam/openfoam4-paraview50 Image of OpenFOAM v4 and ParaView 5.0.1 on... 1
docker.io docker.io/openfoam/openfoam5-graphical-apps Image of OpenFOAM v5 on Ubuntu 16.04 from ... 1
docker.io docker.io/openfoam/openfoam6-graphical-apps Image of OpenFOAM v6 on Ubuntu 18.04 from ... 1
docker.io docker.io/unifem/openfoam-ccx Docker Image for OpenFOAM and Calculix 1 [OK]
docker.io docker.io/nerdalize/openfoam This image makes it easy to run OpenFOAM o... 0 [OK]
docker.io docker.io/openfoam/openfoam-dev-paraview50 OpenFOAM-dev and ParaView 5.0.1 on Ubuntu ... 0
docker.io docker.io/parallelworks/openfoam OpenFOAM 0
docker.io docker.io/parallelworks/openfoam240_pvpython OpenFOAM240 with Python Paraview 0
docker.io docker.io/parallelworks/openfoam4 OpenFOAM Base Container 0

References:

  1. HOWTO: Secure container/docker environments by managing privileges for admins and users
  2. How to fix docker: Got permission denied while trying to connect to the Docker daemon socket