Error: gdal-config not found while installing R dependent packages whereas gdal is installed

Please point out the point that I am missing: openSUSE 11.3 [email protected]:~/Desktop/R> sudo R CMD INSTALL rgdal_0.7-12.tar.gz root's password: * installing to library...

Setting up OpenMPI-1.10.2 to run jobs on multiple nodes

First of all my setup till now: I'm working on a fresh installed Ubuntu Gnome 15.10. on all pc's. My networks consists of 4 pc's with static ips (198.168.0.1 - 198.168.0.4) with 198.168.0.4 as the...

Can't install mpi4py with OpenMPI: Cannot compile MPI programs

it's my first post here so apologies if my style is wrong! I've been trying to install mpi4py (as SU2 requires it for parallel processing) on Ubuntu 16.04 using python 3.6. I downloaded mpi4py...

python subprocess.call can not find dylib in mac

I have a C++ program using Intel-mkl, after compiling the code (assume the executable is a.out), I can run it in terminal /Users/hshi/test/a.out which works perfectly fine. If I use python...

Install the glibc report configure LD_LIBRARY_PATH error

Install the glibc-2.17 on redhat, download, unzip, configure then report LD_LIBRARY_PATH error: checking for gawk... gawk checking version of gawk... 3.1.7, ok checking for nm... nm checking for...

Syntax error near unexpected token '(', when sourcing bashrc to setup Openfoam environment

Recently I installed Bash on Ubuntu on Windows using WSL to use OpenFOAM. But when I installed OpenFOAM it is giving me the error like: -bash: eval: line 38: syntax error near unexpected token...

Install OpenMPI on Ubuntu 17.10

I am using the following command for OpenMPI installation on Ubuntu 17.10: sudo apt-get install openmpi-bin openmpi-common openssh-client openssh-server libopenmpi1.3 libopenmpi-dbg...

Cuda Runtime Error cudaErrorNoDevice: no CUDA-capable device is detected

I am using Chainer, Cupy for CUDA 8.0 . I am trying to train machine learning model using python3.5 script, but I got this error: cupy.cuda.runtime.CUDARuntimeError: cudaErrorNoDevice: no...

Testing MPI project (compiling using Cmake) with Travis CI

I am learning to use Travis CI for continuous integration. My project needs to use the MPI library so I let Travis install OpenMPI and use cmake to compile the code. Here is my .travis.yml...

Slurm sbatch for a PyTorch script draining node; gres/gpu: count changed for node node002 from 0 to 1

We have a user whose script always drains a node. Note this error: "gres/gpu: count changed for node node002 from 0 to 1" Could it be misleading? What could cause the node to drain? Here are the...

How to remove the error: pcl/memory.h: No such file or directory while building c++ file?

I am trying to make this tutorial work for Various Point Cloud of Faces. I did found this and this answer, but can't seem to make them work for my case. I am trying to execute the "CMake" and...

Ubuntu 16.04: -sh: source: not found

I updated my .bashrc. After that, when I tried source ~/.bashrc to make it works, I got: -sh: 13: source: not found I have reviewed the suggestions on...

mpicxx: Command not found

I am very new to linux. I am trying to build lammps open source software with user defined modules that require to build mpi executable on opensuse leap 15.1. lammps -...

MPI complile error, undefined reference to `MPI::Win::Free()

I trying to compile a code written mostly in Fortran with some parts in C, the use some libraries such HDF5 and MPI and probably is written using openmpi 3.2.1 but i have openmpi 4.0.3 installed...

OpenMPI-bin error after update (K)Ubuntu 18.04 to 20.04

I have just upgraded my Kubuntu from 18.04 to 20.04. Unfortunately there is an error that keeps showing up everytime I use apt upgrade or installing something with apt. The error...

Job fails while using srun or mpirun in slurm

I am trying to submit a job with slurm. However, the job fails if I use srun or mpirun. However, it runs fine with mpiexec, albeit running with only single process despite multiple nodes and...

Could NOT find MPI_C and MPI cmake on Ubuntu 18.04

- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") -- Checking for module 'libusb-1.0>=1.0.17' -- Found libusb-1.0, version 1.0.21 -- Checking for module 'opencv>=3.0' -- Found...

mpif90 not found but it's intsalled

I'm trying to run a makefile and came across two errors. When I run make I get this: $ make mpif90 -xHost -ip -fpp -O3 -align -I/include/intel64/lp64 -I/include/fftw -c integ-Coul.F make: mpif90:...

ncap2: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory

I tried to install nco in a remote server (RHEL 7.8) and I am not the root which means I can't use the sudo or yum in the terminal. Then I followed the instructions on the main page on nco...

sbatch: error: Batch job submission failed: Requested node configuration is not available

The problem is not related to the number of the CPU assigned to the job. Before this problem, I had an error with the Nvidia driver configuration in a way that I couldn't detect the GPUs by...

Can't locate Data/Dumper.pm when building dssp - perl is installed but cannot be found?

I am trying to build dssp (https://github.com/cmbi/dssp) on a server-node (not on server-login), and I am facing a problem with how the system finds dependencies. I am working on a centos 7. The...

Python code takes longer to run with MPI (SLURM) than as a single process

I have some python code which takes approximately 12 hours to run on my laptop (MacOS 16GB 2133 MHz LPDDR3). The code is looping over a few thousand iterations and doing some intensive processing...

Fortran compiler not found when configuring

I am trying to install some code on my Mac (10.15.7). I follow the instructions and do ./waf configure --install_all_deps But I get No suitable fortran compiler found (cause: 'cannot determine...

pynestkernel ImportError: libmpi_cxx.so.20: cannot open shared object file: No such file or directory

When installing NEST 2.18 with: cmake \ -Dwith-mpi=/usr/lib/x86_64-linux-gnu/openmpi \ -Dwith-python=3 \ -DPYTHON_EXECUTABLE=/home/robin/.pyenv/versions/3.8.6/bin/python \ ...

docker-compose and Dockerfile do not install drupal

New to docker and I wanted to install Drupal 7 with docker, to mirror our production server environment. (We are getting ready to upgrade to Drupal 8 - not relevant to this question here.) When I...

Problems with Orca and OpenMPI for parallel jobs

Hello to the community: I recently started to use ORCA software for some quantum calculation but I have been having a lot of problems to lunch a parallel calculation in the cluster of my...

Unable to install perl modules via cpanm in conda environments

I'm trying to install perl modules via cpanm inside conda environment with perl installed. The conda environment was build with following definition: name: perl_env channels: - bioconda -...

Fatal Error: mpi.h No such file or directory

I'm a new linux user. I'm getting this error during compilation. When I use the 'make' command within a build directory. Fatal Error: mpi.h No such file or directory I've installed OpenMpi using...

What am I missing getting mpirun to schedule across multiple nodes?

TL;DR; I'm having troubles getting MPI to schedule jobs across more than a single node. There seems to be a communication error between nodes at the MPI level that isn't a problem for TCP or at...

Switch from MPICH to OpenMPI

I have both mpich and openmpi in my Ubuntu 20.04. $ dpkg -l | grep mpi | grep lib ... ii libmpich-dev:amd64 3.3.2-2build1 amd64 ...