Installing Julia Programming Language on CentOS 7

Step 1: The latest Julia Programming language binary can be found at downloaded at

% wget https://julialang-s3.julialang.org/bin/linux/x64/1.5/julia-1.5.3-linux-x86_64.tar.gz

Step 2: Extract the Julia Tar GZ

% tar -zxvf julia-1.5.3-linux-x86_64.tar.gz

Step 3: Move the unpacked folder to /usr/local

% mv julia-1.5.3 /usr/local

Try Julia

Compiling Quantum ESPRESSO-6.7.0 with BEEF and Intel MPI 2018 on CentOS 7

Step 1: Download Quantum ESPRESSO 6.5.0 from Quantum ESPRESSO v. 6.7

% tar -zxvf q-e-qe-6.7.0.tar.gz

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

export MKLROOT=/usr/local/intel_2018/mkl/lib
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 3a: Install libbeef

  1. Installing libbeef with Intel Compilers

Step 3b: 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 LDFLAGS="-L/usr/local/intel/2018u3/mkl/lib/intel64"
#export CPPLAGS="-I/usr/local/intel/2018u3/mkl/include/fftw"
export BEEF_LIBS="-L/usr/local/libbeef-0.1.3/src -lbeef"
export BLAS_LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
export LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64"
export SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64"
#export FFT_LIBS="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_scalapack_lp64"
./configure --enable-parallel --enable-openmp --enable-shared --with-libbeef=yes --with-scalapack=intel --prefix=/usr/local/espresso-6.7.0 | tee Configure.out
% ./setup.sh
% make all
% make install

(I prefer make all without the “make all -j 16” so I can see all the errors and trapped seriously)

If successful, you will see in your bin folder

Using qperf to measure network bandwidth and latency

qperf is a network bandwidth and latency measurement tool which works over many transports including TCP/IP, RDMA, UDP and SCTP

Step 1: Installing qperf on both Server and Client

Server> # yum install qperf
Client> # yum install qperf

Step 2: Open Up the Firewall on the Server

# firewall-cmd --permanent --add-port=19765-19766/tcp
# firewall-cmd --reload

The Server listens at TCP Port 19765 by default. Do note that once qperf makes a connection, it will create a control port and data port , the default data port is 19765 but we also need to enable a data port to run test which can be 19766.

Step 3a: Have the Server listen (as qperf server)

Server> $ qperf

Step 4: Connect to qperf Server with qperf Client and measure bandwidth

Client > $ qperf -ip 19766 -t 60 qperf_server_ip_address tcp_bw
tcp_bw:
    bw  =  2.52 GB/sec

Step 5: Connect to qperf Server with qperf Client and measure latency

qperf -vvs qperf_server_ip_address tcp_lat
tcp_lat:
latency = 20.7 us
msg_rate = 48.1 K/sec
loc_send_bytes = 48.2 KB
loc_recv_bytes = 48.2 KB
loc_send_msgs = 48,196
loc_recv_msgs = 48,196
rem_send_bytes = 48.2 KB
rem_recv_bytes = 48.2 KB
rem_send_msgs = 48,197
rem_recv_msgs = 48,197

References:

  1. How to use qperf to measure network bandwidth and latency performance?

How to configure NFS on CentOS 7

Step 1: Do a Yum Install

# yum install nfs-utils rpcbind

Step 2: Enable the Service at Boot Time

# systemctl enable nfs-server
# systemctl enable rpcbind
# systemctl enable nfs-lock     (it does not need to be enabled since rpc-statd.service  is static.)
# systemctl enable nfs-idmap    (it does not need to be enabled since nfs-idmapd.service is static.)

Step 3: Start the Services

# systemctl start rpcbind
# systemctl start nfs-server
# systemctl start nfs-lock
# systemctl start nfs-idmap

Step 4: Confirm the status of NFS

# systemctl status nfs

Step 5: Create a mount point

# mkdir /shared-data

Step 6: Exports the Share

# vim /etc/exports
/shared-data 192.168.0.0/16(rw,no_root_squash)

Step 7: Export the Share

# exportfs -rv

Step 8: Restart the NFS Services

# systemctl restart nfs-server

Step 9: Configure the Firewall

# firewall-cmd --add-service=nfs --zone=internal --permanent
# firewall-cmd --add-service=mountd --zone=internal --permanent
# firewall-cmd --add-service=rpc-bind --zone=internal --permanent

References:

  1. How to configure NFS in RHEL 7
  2. What firewalld services should be active on an NFS server in RHEL 7?

Performance Required for Deep Learning

There is this question that I wanted to find out about deep learning. What are essential System, Network, Protocol that will speed up the Training and/or Inferencing. There may not be necessary to employ the same level of requirements from Training to Inferencing and Vice Versa. I have received this information during a Nvidia Presentation

Training:

  1. Scalability requires ultra-fast networking
  2. Same hardware needs as HPC
  3. Extreme network bandwidth
  4. RDMA
  5. SHARP (Mellanox Scalable Hierarchical Aggregation and Reduction Protocol)
  6. GPUDirect (https://developer.nvidia.com/gpudirect)
  7. Fast Access Storage

Influencing

  1. Highly Transactional
  2. Ultra-low Latency
  3. Instant Network Response
  4. RDMA
  5. PeerDirect, GPUDirect

 

 

Configuring External libraries for R-Studio for CentOS 7

RStudio can be configured by adding entries to 2 configuration files. It may not exist by default and you may need to create

/etc/rstudio/rserver.conf
/etc/rstudio/rsession.conf

If you need to add additional libraries to the default LD_LIBRARY_PATH for R sessions. You have to add the parameters to the /etc/rstudio/rserver.conf

Step 1: Enter External Libraries settings
For example, you may want to add GCC-6.5 libraries

# Server Configuration File
rsession-ld-library-path=/usr/local/gcc-6.5.0/lib64:/usr/local/gcc-6.5.0/lib

Step 2a: Stop the R Server Services

# /usr/sbin/rstudio-server stop

Step 2b: Verify the Installation

# rstudio-server verify-installation

Step 2c: Start the R Server Services

# /usr/sbin/rstudio-server start
# /usr/sbin/rstudio-server status

(Make sure there is no error)

References:

  1. RStudio Server: Configuring the Server

 

AlmaLinux Enterprise-Grade Server OS compatible with RHEL 8

What is AlmaLinux? According to the website https://almalinux.org/

AlmaLinux is an enterprise-grade server OS, a stable Linux distribution with regular releases that come with long support windows. You can rely on AlmaLinux to run you and your clients’ critical workloads.

  • Fedora-like distribution based on a precise RHEL clone
  • Production-ready and stable, matching RHEL features 1:1
  • Enjoy the predictability of a stable release issued in tandem with RHEL