Installation on cluster CentOS


#1

Hi all,

I am trying to install ASPECT on the cluster (CentOS 6.7). I have already downloaded it and run it properly on my workstation. But somehow I have failed to install deal_ii on the cluster. I am using ‘candi’ to do the installation.

I already installed the pre-required dependencies but the compilation of deal_ii end up with an error highlighted bellow-

"This is candi (compile and install)

Project: deal.II-toolchain: Found configuration.
using (user-forced) ./deal.II-toolchain/platforms/supported/centos7.platform.

Operating System Type detected as: linux
Dynamic shared library file extension detected as: *.so


Please read carefully your operating system notes below!

CentOS 7

This build script assumes that you have several packages already
installed via CentOS’s yum using the following command:

sudo yum install patch svn git wget
@development-tools gcc-c++ cmake
openmpi openmpi-devel
patch
libtool libtool-ltdl libtool-ltdl-devel
lua lua-devel
blas blas-devel lapack lapack-devel
doxygen graphviz graphviz-devel qt-devel

Please load the ‘openmpi’ compiler with
module load mpi/openmpi-x86_64 and then set the compiler enviroment variables to export CC=mpicc; export CXX=mpicxx; export FC=mpif90; export FF=mpif77
before you continue!


Please make sure you’ve read the instructions above and your system
is ready for installing deal.II-toolchain.
If not, please abort the installer by pressing + !
Then copy and paste these instructions into this terminal.

Once ready, hit enter to continue!


candi tries now to download, configure, build and install:

Project: deal.II-toolchain
Platform: deal.II-toolchain/platforms/supported/centos7.platform


Downloading files to: /source/candi-master/deal.ii-candi/tmp/src
Unpacking files to: /source/candi-master/deal.ii-candi/tmp/unpack
Building packages in: /source/candi-master/deal.ii-candi/tmp/build
Installing packages in: /source/candi-master/install/candi
Package configuration in: /source/candi-master/install/candi/configuration


Number of (at most) build processes to use: PROCS=12


Packages:
load:dealii-prepare
once:opencascade
once:parmetis
once:hdf5
once:p4est
once:petsc
once:slepc
dealii


Building stable releases of deal.II-toolchain packages.


Currently loaded modulefiles:
No Modulefiles Currently Loaded.

Compiler Variables:

CC variable not set, but default mpicc found.
CC = /opt/openmpi/bin/mpicc
CXX variable not set, but default mpicxx found.
CXX = /opt/openmpi/bin/mpicxx
FC variable not set, but default mpif90 found.
FC = /opt/openmpi/bin/mpif90
FF variable not set, but default mpif77 found.
FF = /opt/openmpi/bin/mpif77


Once ready, hit enter to continue!


candi tries now to download, configure, build and install:

Project: deal.II-toolchain
Platform: deal.II-toolchain/platforms/supported/centos7.platform

Loading dealii-prepare
Skipping opencascade
Skipping parmetis
Skipping hdf5
Skipping p4est
PETSc: configuration with ParMETIS
Skipping petsc
Skipping slepc
deal.II: configuration with METIS
deal.II: configuration with P4EST
deal.II: configuration with HDF5
deal.II: configuration with PETSC
deal.II: configuration with SLEPC
deal.II: configuration with OPENCASCADE
Fetching dealii v9.0.0
Initialized empty Git repository in /source/candi-master/deal.ii-candi/tmp/unpac k/deal.II-v9.0.0/.git/
error: while accessing https://github.com/dealii/dealii.git/info/refs

fatal: HTTP request failed
Failure with exit status: 128
Exit message: candi: git clone https://github.com/dealii/dealii.git deal.II-v9.0 .0 failed"

Could you please provide us any information in this regard?

Thanks for the help!
Regards
Joy


#2

Hi Joy,

Apparently, your git clone command failed. You may want to be sure you can access internet from the cluster. I had to specify the http_proxy and https_proxy on the cluster in my institution to allow git clone to work! Everything should work fine when you can clone things.
In case you can’t clone, then I believe you can download things from github and put them on your cluster with rsync or scp and start by specifying where they are.

Best
Marine


#3

Adding to Marine’s suggestion (see if git clone https://github.com/dealii/dealii.git works if you do it manually anywhere on your cluster), I see two funny spaces in the first line (un pack) and last line (deal.II-v9.0 .0) of your posted output. If those are not just copy-paste artifacts and they actually exist in your output you will want to check how they got there (e.g. accidentally placing them in the installation path argument of candi or in candi.cfg).

Hope that helps.
Best,
Rene


#4

Hi Marine,

Thank you for you information.

I can access internet from the cluster. The issue might have appeared due to those proxy issues. I have asked my university to specify my proxy on the cluster. I will try to install it .

Hope this time it will work!

Best
Joy


#5

Hi Rene,

Yes, Those are copy-paste artifacts. I have checked the output. It seems okay.

Best
Joy