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Installing CP2K with Nvidia HPCX on Rocky Linux 8.5

What is HPCX?

NVIDIA® HPC-X® is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages. For more information, do take a look at https://developer.nvidia.com/networking/hpc-x

What is CP2K?

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, …), and classical force fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimisation, and transition state optimization using NEB or dimer method. (Detailed overview of features.). For more information, do take a look at https://www.cp2k.org/

Getting the CP2K

git clone --recursive https://github.com/cp2k/cp2k.git cp2k

Unpack hpcx and Optimised OpenMPI Libraries. For more information on installation, do take a look at Installing and Loading HPC-X

Extract hpcx.tbz into your current working directory.

% tar -xvf hpcx.tbz
% cd hpcx
% export HPCX_HOME=$PWD
% module use $HPCX_HOME/modulefiles
% module load hpcx

Use the CP2K Toolchain to Compile for the easiest

% cd cp2k
% cd /usr/local/software/cp2k/tools/toolchain
% ./install_cp2k_toolchain.sh --no-check-certificate --with-openmpi

Compiling the CP2K

.....
.....
==================== generating arch files ====================
arch files can be found in the /usr/local/software/cp2k/tools/toolchain/install/arch subdirectory
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.ssmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_static.ssmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.sdbg
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_coverage.sdbg
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.psmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.pdbg
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_static.psmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_warn.psmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_coverage.pdbg
========================== usage =========================
Done!
Now copy:
  cp /usr/local/software/cp2k/tools/toolchain/install/arch/* to the cp2k/arch/ directory
To use the installed tools and libraries and cp2k version
compiled with it you will first need to execute at the prompt:
  source /usr/local/software/cp2k/tools/toolchain/install/setup
To build CP2K you should change directory:
  cd cp2k/
  make -j 80 ARCH=local VERSION="ssmp sdbg psmp pdbg"

Do exactly on the ending instruction 

% cp /usr/local/software/cp2k/tools/toolchain/install/arch/* /usr/local/cp2k/arch
% source /usr/local/software/cp2k/tools/toolchain/install/setup
% cd /usr/local/software/cp2k
% make -j 32 ARCH=local VERSION="ssmp sdbg psmp pdbg"

If you encounter an error during making like the one below, just do an install for liblsan

% /usr/bin/ld: cannot find /usr/lib64/liblsan.so.0.0.0
% dnf install liblsan -y

If you encounter error like the ones below for fftw libraries, 

/usr/bin/ld: cannot find -lfftw3_mpi
collect2: error: ld returned 1 exit status

You have to go to the supporting package libraries and do some editing.

% cd /usr/local/software/cp2k/tools/toolchain/install/fftw-3.3.10/lib
% ln -s libfftw3.a libfftw3_mpi.a
% ln -s libfftw3.la libfftw3_mpi.la

Try again

% cd /usr/local/software/cp2k
% make -j 32 ARCH=local VERSION="ssmp sdbg psmp pdbg"

If successful, you should see binaries at /usr/local/software/cp2k/exe/local

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GCCGO Error During GCC-10.4.0 Compilation on CentOS 7

If you encounter “gccgo: error: ../x86_64-pc-linux-gnu/libgo/libgotool.a: No such file or directory”

.....
.....
/home/user1/gcc-10.4.0/host-x86_64-pc-linux-gnu/gcc/gccgo -B/home/user1/gcc-10.4.0/host-x86_64-pc-linux-gnu/gcc/ -B/usr/x86_64-pc-linux-gnu/bin/ -B/usr/x86_64-pc-linux-gnu/lib/ -isystem /usr/x86_64-pc-linux-gnu/include -isystem /usr/x86_64-pc-linux-gnu/sys-include   -g -O2 -I ../x86_64-pc-linux-gnu/libgo -static-libstdc++ -static-libgcc  -L ../x86_64-pc-linux-gnu/libgo -L ../x86_64-pc-linux-gnu/libgo/.libs -o go ../.././gotools/../libgo/go/cmd/go/alldocs.go ../.././gotools/../libgo/go/cmd/go/go11.go ../.././gotools/../libgo/go/cmd/go/main.go ../x86_64-pc-linux-gnu/libgo/libgotool.a  
gccgo: error: ../x86_64-pc-linux-gnu/libgo/libgotool.a: No such file or directory
make[2]: *** [Makefile:821: go] Error 1
make[2]: Leaving directory '/home/user1/gcc-10.4.0/host-x86_64-pc-linux-gnu/gotools'
make[1]: *** [Makefile:14649: all-gotools] Error 2
make[1]: Leaving directory '/home/user1/gcc-10.4.0'
make: *** [Makefile:997: all] Error 2

The issue can be easily resolved by not building gcc in the same directory as the source code. At GCC Home

% ./contrib/download_prerequisites
% mkdir build
% ../configure --prefix=/usr/local/gcc-10.4.0 --disable-multilib --enable-languages=all
% make -j 8
% make install
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Compiling GCC-10.4.0 on CentOS-7

Step 1: Download the TarBall version of GCC version. If you want to take look at all the available versions, you can take a look at http://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/

For this blog entry, we will install GCC-10.4.0. First thing first, let’s get the Tarball

% wget http://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/gcc-10.4.0/gcc-10.4.0.tar.gz

Step 2: Make sure the bzip2 is available in the System

% yum install bzip2 bzip2-devel

Step 3: Untar the TarBall 

% tar -zxvf gcc-10.4.0.tar.gz
% cd gcc-10.4.0

Step 4: Download the prerequisites and start configuring the GCC

% ./contrib/download_prerequisites
% ./configure --prefix=/usr/local/gcc-10.4.0 --disable-multilib --enable-languages=all
% make -j 8
% make install

Step 5: Verify the Installation

% gcc --version
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Compiling VASP.6.3.0 with GPGPU Capability using Nvidia HPC-SDK on Rocky Linux 8.5

To Compile VASP with GPGPU Capability using Nvidia HPC-SDK. For more information, do take a look at VASP – Install VASP.6.X.X

VASP support several compilers. But we will be focusing on Nvidia HPC-SDK only for this blog. To download the NVIDIA HPC-SDK

To compile Nvidia HPC SDK, do take a look at HPC SDK Documentation

% tar -xpfz <tarfile>.tar.gz

You may want to use modulefiles provided at hpc-sdk if you are using Module Environment

% module use /usr/local/nvidia/hpc_sdk/modulefiles

You should be able to see something like

------------------- /usr/local/nvidia/hpc_sdk/modulefiles ---------------
nvhpc-byo-compiler/22.5  nvhpc-nompi/22.5  nvhpc/22.5

You can untar the VASP.6.3.3. and potpaw_PBE.54

% tar -xvf vasp.6.3.0.tar
% tar -xvf potpaw_PBE.54.tar

At the installation base of vasp.6.3.0 base

% cp arch/makefile.include.nvhpc_ompi_mkl_omp_acc ./makefile.include

Load the Nvidia GPGPU SDK and compile. If you are using OneAPI Intel Compilers, you can use module use after compilation. It will not be covered in this write-up.

% module use /usr/local/intel/oneapi-2022/modulefiles
% module load nvhpc/22.5
% module load mkl/latest
% make veryclean
% make DEPS=1 -j

If during the make, you encounter the error

/usr/local/nvidia/hpc_sdk/Linux_x86_64/22.5/comm_libs/openmpi/openmpi-3.1.5/bin/.bin/mpif90: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory

You can dnf install libatomic

% dnf install libatomic -y

Try Compiling again

References:

  1. Installing VASP.6.X.X
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Changes to SSH Server on DevCloud

When connecting to the DevCloud for oneAPI

$ ssh devcloud @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY! Someone could be eavesdropping on you right now (man-in-the-middle attack)! It is also possible that a host key has just been changed. The fingerprint for the ED25519 key sent by the remote host is SHA256:/Dlip01tdMyRmhMDc870Z4Uk7AancwwoTnbb0EZajK0. Please contact your system administrator. Add correct host key in /home/<user_name>/.ssh/known_hosts to get rid of this message. Offending ECDSA key in /home/<user_name>/.ssh/known_hosts:# Host key for ssh.devcloud.intel.com has changed and you have requested strict checking. Host key verification failed. kex_exchange_identification: Connection closed by remote host Connection closed by UNKNOWN port 65535

Cause:

DevCloud have just migrated oneAPI DevCloud to a new SSH tunnel server and upgraded the SSH server version to OpenSSH _8.2p1. For this reason the DevCloud are unable to reuse the old SSH fingerprint for the new server.

Remediation:

Step 1: Remove the Offending FingerPrint(s)

Method 1: rename your existing ~/.ssh/known_hosts file to something else, such as ~/.ssh/known_hosts.yymmdd

$ mv ~/.ssh/known_hosts ~/.ssh/known_hosts.220623

Method 2: remove the offending host SSH fingerprint only:

$ ssh-keygen -R ssh.devcloud.intel.com # Host ssh.devcloud.intel.com found: line 1 # Host ssh.devcloud.intel.com found: line 2 # Host ssh.devcloud.intel.com found: line 3 /home/<user_name>/.ssh/known_hosts updated. Original contents retained as /home/<user_name>/.ssh/known_hosts.old

Step 2: reconnect to the DevCloud and accept the new key.

$ ssh devcloud The authenticity of host 'ssh.devcloud.intel.com (12.229.61.118)' can't be established. ED25519 key fingerprint is SHA256:/Dlip01tdMyRmhMDc870Z4Uk7AancwwoTnbb0EZajK0. This key is not known by any other names Are you sure you want to continue connecting (yes/no/[fingerprint])? yes Warning: Permanently added 'ssh.devcloud.intel.com' (ED25519) to the list of known hosts.
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Intel Distribution OpenVINO Toolkit 2022.1 is available!

For more information, do take a look at Intel® Distribution of OpenVINO™ Toolkit

Updated, Cleaner API

  • The new OpenVINO API 2.0 was introduced, which aligns OpenVINO inputs and outputs with frameworks. Input and output tensors use native framework layouts and element types. 
  • The API parameters in Model Optimizer have been reduced to minimize complexity. Performance has been significantly improved for model conversion on Open Neural Network Exchange (ONNX*) models.

Broader Model Support

  • With Dynamic Input Shapes capabilities on CPU, OpenVINO is able to adapt to multiple input dimensions in a single model providing more complete NLP support. Support for Dynamic Shapes on additional XPUs is expected in a future dot release.
  • New models with a focus on NLP and a new category, Anomaly Detection, and support for conversion and inference of select PaddlePaddle* models:
    • Pretrained models for anomaly segmentation focus on industrial inspection making speech denoising trainable, plus updates on speech recognition and speech synthesis
    • Combined demonstration that includes noise reduction, speech recognition, question answering, translation, and text to speech
    • Public models with a focus on NLP ContextNet, Speech-Transformer, HiFi-GAN, Glow-TTS, FastSpeech2, and Wav2Vec

Portability and Performance

  • New AUTO plug-in self-discovers available system inferencing capacity based on model requirements so applications no longer need to know their compute environment in advance.
  • Automatic batching functionality via code hints automatically scale batch size based on XPU and available memory.
  • Built with 12th generation Intel® Core™ processors (formerly code named Alder Lake) in mind. Supports the hybrid architecture necessary to deliver enhancements for high performance inferencing on CPUs and integrated GPUs.
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No matching repo to modify: PowerTools when using dnf install on Rocky Linux 8.5

I was trying to install hdf5 after enabling EPEL. Installing EPEL

% dnf install -y epel-release
% dnf config-manager --set-enabled PowerTools
Error: No matching repo to modify: PowerTools.

I’ve noticed this documentation from CentOS-8 Repoid, there are name changes from Yum_repo_file_and_repoid_changes from 8.3 onwards. The documents can be found at https://wiki.centos.org/Manuals/ReleaseNotes/CentOS8.2011#Yum_repo_file_and_repoid_changes

Repoid (8.2.2004 and before)Repoid (8.3.2011 and later)
BaseOSbaseos
AppStreamappstream
PowerToolspowertools
centosplusplus
HighAvailabilityha
base-debuginfodebuginfo
Develdevel
BaseOS-sourcebaseos-source
AppStream-sourceappstream-source
centosplus-sourceplus-source
base-debuginfodebuginfo
% dnf config-manager --set-enabled powertools
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Cannot install the best candidate for the job for CUDA Drivers and Rocky Linux 8.5

I follow the blog Installing Nvidia Drivers on Rocky Linux 8.5. But I encountered an error that I have not encountered before

Error:
 Problem 1: package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64
 Problem 2: package cuda-drivers-515.48.07-1.x86_64 requires nvidia-kmod >= 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64
 Problem 3: package nvidia-driver-3:515.48.07-1.el8.x86_64 requires nvidia-kmod-common = 3:515.48.07, but none of the providers can be installed
  - package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64
 Problem 4: package nvidia-driver-3:515.48.07-1.el8.x86_64 requires nvidia-kmod-common = 3:515.48.07, but none of the providers can be installed
  - package nvidia-modprobe-3:515.48.07-1.el8.x86_64 requires nvidia-driver(x86-64) = 3:515.48.07, but none of the providers can be installed
  - package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64
 Problem 5: package nvidia-driver-3:515.48.07-1.el8.x86_64 requires nvidia-kmod-common = 3:515.48.07, but none of the providers can be installed
  - package nvidia-settings-3:515.48.07-1.el8.x86_64 requires nvidia-driver(x86-64) = 3:515.48.07, but none of the providers can be installed
  - package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64
 Problem 6: package nvidia-driver-3:515.48.07-1.el8.x86_64 requires nvidia-kmod-common = 3:515.48.07, but none of the providers can be installed
  - package nvidia-xconfig-3:515.48.07-1.el8.x86_64 requires nvidia-driver(x86-64) = 3:515.48.07, but none of the providers can be installed
  - package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - nothing provides dkms needed by kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64

The hint is that dkms is required.

nothing provides dkms needed by kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64

Enable EPEL Repository

# dnf install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm
 # dnf config-manager --enable epel

Install dkms

 # dnf install dkms*

Install the latest Nvidia Drivers (If possible).

# dnf module install nvidia-driver:latest

If the Error pop out like this 

Last metadata expiration check: 0:01:01 ago on Mon 06 Jun 2022 08:47:40 PM EDT.
Error:
 Problem 1: package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
 Problem 2: package cuda-drivers-515.48.07-1.x86_64 requires nvidia-kmod >= 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
 Problem 3: package nvidia-driver-3:515.48.07-1.el8.x86_64 requires nvidia-kmod-common = 3:515.48.07, but none of the providers can be installed
  - package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
 Problem 4: package nvidia-driver-3:515.48.07-1.el8.x86_64 requires nvidia-kmod-common = 3:515.48.07, but none of the providers can be installed
  - package nvidia-modprobe-3:515.48.07-1.el8.x86_64 requires nvidia-driver(x86-64) = 3:515.48.07, but none of the providers can be installed
  - package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
 Problem 5: package nvidia-driver-3:515.48.07-1.el8.x86_64 requires nvidia-kmod-common = 3:515.48.07, but none of the providers can be installed
  - package nvidia-settings-3:515.48.07-1.el8.x86_64 requires nvidia-driver(x86-64) = 3:515.48.07, but none of the providers can be installed
  - package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
 Problem 6: package nvidia-driver-3:515.48.07-1.el8.x86_64 requires nvidia-kmod-common = 3:515.48.07, but none of the providers can be installed
  - package nvidia-xconfig-3:515.48.07-1.el8.x86_64 requires nvidia-driver(x86-64) = 3:515.48.07, but none of the providers can be installed
  - package nvidia-kmod-common-3:515.48.07-1.el8.noarch requires nvidia-kmod = 3:515.48.07, but none of the providers can be installed
  - cannot install the best candidate for the job
  - package kmod-nvidia-latest-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering
  - package kmod-nvidia-open-dkms-3:515.48.07-1.el8.x86_64 is filtered out by modular filtering

You will notice that the dkms issues has been resolved. Try not using the nvidia-driver:latest

# dnf module install nvidia-driver
===================================================================================================================================================
 Package                                Architecture        Version                                           Repository                      Size
===================================================================================================================================================
Upgrading:
 bcc                                    x86_64              0.19.0-5.el8                                      appstream                      674 k
 bcc-tools                              x86_64              0.19.0-5.el8                                      appstream                      447 k
 bpftrace                               x86_64              0.12.1-4.el8                                      appstream                      1.3 M
 clang-libs                             x86_64              13.0.1-1.module+el8.6.0+825+7e27476a              appstream                       23 M
 clang-resource-filesystem              x86_64              13.0.1-1.module+el8.6.0+825+7e27476a              appstream                       13 k
 compiler-rt                            x86_64              13.0.1-1.module+el8.6.0+825+7e27476a              appstream                      4.2 M
 libglvnd                               x86_64              1:1.3.4-1.el8                                     appstream                      126 k
 libglvnd-egl                           x86_64              1:1.3.4-1.el8                                     appstream                       48 k
 libglvnd-gles                          x86_64              1:1.3.4-1.el8                                     appstream                       39 k
 libglvnd-glx                           x86_64              1:1.3.4-1.el8                                     appstream                      136 k
 libomp-devel                           x86_64              13.0.1-1.module+el8.6.0+825+7e27476a              appstream                       28 k
 llvm-libs                              x86_64              13.0.1-1.module+el8.6.0+825+7e27476a              appstream                       24 M
 mesa-dri-drivers                       x86_64              21.3.4-1.el8                                      appstream                       11 M
 mesa-filesystem                        x86_64              21.3.4-1.el8                                      appstream                       33 k
 mesa-libxatracker                      x86_64              21.3.4-1.el8                                      appstream                      2.0 M
 python3-bcc                            x86_64              0.19.0-5.el8                                      appstream                       89 k
Installing group/module packages:
 cuda-drivers                           x86_64              515.48.07-1                                       cuda-rhel8-x86_64              8.1 k
 kmod-nvidia-latest-dkms                x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               30 M
 nvidia-driver                          x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               23 M
 nvidia-driver-NVML                     x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64              462 k
 nvidia-driver-NvFBCOpenGL              x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               54 k
 nvidia-driver-cuda                     x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64              455 k
 nvidia-driver-cuda-libs                x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               54 M
 nvidia-driver-devel                    x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               13 k
 nvidia-driver-libs                     x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64              177 M
 nvidia-kmod-common                     noarch              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               13 k
 nvidia-libXNVCtrl                      x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               26 k
 nvidia-libXNVCtrl-devel                x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               56 k
 nvidia-modprobe                        x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               37 k
 nvidia-persistenced                    x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64               43 k
 nvidia-settings                        x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64              835 k
 nvidia-xconfig                         x86_64              3:515.48.07-1.el8                                 cuda-rhel8-x86_64              106 k
Installing dependencies:
 dnf-plugin-nvidia                      noarch              2.0-1.el8                                         cuda-rhel8-x86_64               12 k
 egl-wayland                            x86_64              1.1.9-3.el8                                       appstream                       39 k
 libX11-devel                           x86_64              1.6.8-5.el8                                       appstream                      975 k
 libXau-devel                           x86_64              1.0.9-3.el8                                       appstream                       19 k
 libglvnd-opengl                        x86_64              1:1.3.4-1.el8                                     appstream                       46 k
 libvdpau                               x86_64              1.4-2.el8                                         appstream                       40 k
 libxcb-devel                           x86_64              1.13.1-1.el8                                      appstream                      1.1 M
 mesa-vulkan-drivers                    x86_64              21.3.4-1.el8                                      appstream                      6.7 M
 ocl-icd                                x86_64              2.2.12-1.el8                                      appstream                       50 k
 opencl-filesystem                      noarch              1.0-6.el8                                         appstream                      7.3 k
 vulkan-loader                          x86_64              1.3.204.0-2.el8                                   appstream                      133 k
 xorg-x11-proto-devel                   noarch              2020.1-3.el8                                      appstream                      279 k
Installing module profiles:
 nvidia-driver/default
Enabling module streams:
 nvidia-driver                                              latest-dkms

.....
.....

Finally do a 

# nvidia-smi
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 515.48.07    Driver Version: 515.48.07    CUDA Version: 11.7     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  NVIDIA A100-PCI...  Off  | 00000000:A3:00.0 Off |                    0 |
| N/A   49C    P0    46W / 250W |      0MiB / 40960MiB |      0%      Default |
|                               |                      |             Disabled |
+-------------------------------+----------------------+----------------------+
|   1  NVIDIA A100-PCI...  Off  | 00000000:C3:00.0 Off |                    0 |
| N/A   53C    P0    46W / 250W |      0MiB / 40960MiB |      0%      Default |
|                               |                      |             Disabled |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                                  |
|  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
|        ID   ID                                                   Usage      |
|=============================================================================|
|  No running processes found                                                 |
+-----------------------------------------------------------------------------+
by

Failover feature “HFSS SBR+Solve” is not available. Request name hfssbr_solve does not exist in the licensing pool.

During usage of ANSYS EM, you may encounter issues like the one below.

Fail to enable feature using current license setting. Note that pro, premium, enterprise licenses are available on your server. To use these licenses check the corresponding UI option. For more information, search "PPE" in the help documentation. Failover feature "HFSS SBR+Solve" is not available. Request name hfssbr_solve does not exist in the licensing pool. No such feature exists. Feature: hfssbr_solveLicensepath: 1055@kangkong.hpc.ntu.edu.sg: FlexNet Licensing error:-5,147

The resolution is to activate the correct product licensing which are not activated by default. See the Pix on how to activate the licensingsee less.

by

Compiling Singularity-CE-3.10.0 on Rocky Linux 8

The Official Documentation can be found at https://sylabs.io/guides/3.0/user-guide/installation.html

Prerequisites 1 – Go

Go to the Download Page https://go.dev/dl/ to download the Linux Version.

Extract the archive you downloaded into /usr/local, creating a Go tree in /usr/local/go.

This step below will remove a previous installation at /usr/local/go, if any, prior to extracting. Please back up any data before proceeding.

% rm -rf /usr/local/go && tar -C /usr/local -xzf go1.18.3.linux-amd64.tar.gz

Add /usr/local/go/bin to the PATH environment variable. You can do this by adding the following line to your $HOME/.profile or /etc/profile (for a system-wide installation):

export PATH=$PATH:/usr/local/go/bin

Verify the Installation with the command

% go version

Compiling Singularity

To download Singularity, do visit the download site. Singularity uses a build system called makeit. mconfig is called to generate Makefile and them make is used to compile and install

% git clone https://github.com/sylabs/singularity.git --recurse-submodules
% cd singularity
% ./mconfig --prefix=/usr/local/singularity-ce-3.10.0
% cd builddir
% make
% make install
.....
.....
 checking: header linux/securebits.h... yes
 checking: header linux/capability.h... yes
 checking: libseccomp+headers... yes
 checking: conmon source... no

conmon source not found

Unless you are building --without-conmon you must 'git clone --recurse-submodules'
or 'git submodule update --init'.

You may want to install glib2-devel, delete the singularity directory and make the singularity again. 

% dnf install glib2-devel

Remote the cloned singularity directory and git clone again

% rm -Rv --force singularity
% git clone https://github.com/sylabs/singularity.git --recurse-submodules

Recompile with mconfig again. If successful, it should be something like

=> generating fragments ...
=> building Makefile ...
=> generating singularity-ce.spec ...
=> project singularity-ce setup with :
    - host arch: x86_64
    - host wordsize: 64-bit
    - host C compiler: cc
    - host Go compiler: /usr/local/go-1.18.3/bin/go
    - host system: unix
      ---
    - target arch: x86_64
    - target wordsize: 64-bit
    - target C compiler: cc
      ---
    - config profile: release
      ---
    - SUID install: yes
    - Network plugins: yes
    - seccomp support: yes
    - Build conmon: yes
      ---
    - verbose: no
      ---
    - cryptsetup: /usr/sbin/cryptsetup
      ---
    - version: 3.10.0+21-g1b1a05ff8

% cd builddir
% make
% make install

Testing

As long as you see a cow your installation is working properly…….

% singularity run library://godlovedc/funny/lolcow
< Exercise caution in your daily affairs. >
 -----------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

References:

  1. https://sylabs.io/guides/3.0/user-guide/installation.html
  2. https://github.com/NIH-HPC/Singularity-Tutorial
  3. Compiling Singularity-CE-3.9.2 on CentOS-7