[jyang1]

Hi,

I am struggling to install OpenFOAM 2.3.0 on SSH red hat 6.2 and I am uploading this thread with the hope to get some great advice from you experts. (I am completely new to both RHEL and SSH, and I used OF on my laptop couple of times but that's about it)

So far, I have been following the installation procedure as explained in the link:

http://www.openfoam.org/archive/2.3.0/download/rhel.php

The machine belongs to an institution so I doubt I will be able to change the RHEL version.

The first two command lines from the link seems to work fine except that I can't install both gcc and openmpi (the output states the following: public key for gcc 4.4.7 not installed, and public key for mpirun (openmpi) 1.5 not installed)

From what I've found so far the OF 2.3.0 only works with gcc versions higher than 4.5, so I tried to install higher versions of gcc individually but I failed to do so. I did the same with openmpi but again no luck, although when I check the version of mpirun it does come up (version 1.4.5) so I presumed openmpi was previously installed.

Then the rest of the command lines from the link works fine, but I couldn't download the rpm files via terminal using the command lines:

sudo rpm -i http://www.openfoam.org/download/rhe...0-1.x86_64.rpm

sudo rpm -i http://www.openfoam.org/download/rhe...0-1.x86_64.rpm

sudo rpm -i http://www.openfoam.org/download/rhe...0-1.x86_64.rpm

the outputs for these commands shows that it failed to transmit files from the url, but when I go to the urls they are fine.

I did refer to another link: https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL

but it seems to use something called CentOS, and I am not really aware of what it is. I did try to follow the steps, but still no luck.

I would greatly appreciate if any of you could be able to give a bit of help to get it installed correctly. Any advice is very welcomed.

Thank you kindly.

[wyldckat]

Greetings jyang1 and welcome to posting on the forum!

As the wiki page you indicated, it briefly explains: https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL

Both SL and CentOS derive from RHEL

If you look for CentOS at wikipedia, you'll find this description: https://en.wikipedia.org/wiki/CentOS

CentOS (abbreviated from Community Enterprise Operating System) is a Linux distribution that attempts to provide a free, enterprise-class, community-supported computing platform which aims to be functionally compatible with its upstream source, Red Hat Enterprise Linux (RHEL).

You probably cannot install the RPM packages from the command line because the network connection you're using relies on a proxy server, which the browser is already configured to work with, but the RPM infrastructure isn't configured to do so. After downloading the files, you can run the rpm command directly with the files you've downloaded, e.g.:

sudo rpm -i OpenFOAM-scotch-6.0.0-1.x86_64.rpm

If using the RPM packages still doesn't work, then are you able to use with success the steps #1 and #2 from these instructions: https://openfoamwiki.net/index.php/I...HEL#CentOS_6.6 - It's for OpenFOAM 2.4.0 and CentOS 6.6, but those two steps should be identical for any CentOS and RHEL 6.x versions. Those steps will install the necessary packages that are needed for building OpenFOAM and ParaView from source code.
If you're able to install the packages stated in step #2, then you can follow the remaining instructions; and whenever it tells you to use "wget" (it's for downloading files from the command line), you should download the file manually.



If you cannot install those packages yourself, then ask your systems administrator.

If the administrator cannot install those packages, the only other 2 ways that I know of:

1. One way is probably to resort to installing CentOS 6.2 in a virtual machine and building OpenFOAM inside the virtual machine. Once the build is complete, you can transfer it to the real machine that has RHEL 6.2.
   • You can find instructions on how to transfer the installation from the virtual machine to the real machine here: http://www.cfd-online.com/Forums/ope...tml#post525535 - post #5
2. Another is to use the pre-built versions provided by the CentFOAM project: http://sourceforge.net/projects/centfoam/ - the closest installation instructions I could find right now are these: http://www.cfd-online.com/Forums/ope...tml#post362913

Best regards,Bruno

[wyldckat]

Update: CentFOAM's wiki is back online: http://centfoam.sourceforge.net/wiki....php/Main_Page

[jyang1]

Thank you very much for your reply!

My apologies for such a late reply. I had pretty much given up installing it on the workstation without realising you replied to the thread!

I managed to install OpenFOAM by manually downloading the rpm files as you mentioned, thank you.

The problem I am facing now is that it won't allow me to install openmpi and gcc-gfortran.

If I update the packages using

yum groupinstall 'Development Tools'

it gives me (excluding the other comments for successful downloads):

Downloading Packages:
warning: rpmts_HdrFromFdno: Header V3 RSA/SHA256 Signature, key ID 41a40948: NOKEY


Public key for gcc-gfortran-4.4.7-4.el6.x86_64.rpm is not installed

Also, when I try to install openmpi

yum install openmpi

it gives me

Loaded plugins: product-id, refresh-packagekit, security, subscription-manager
Updating certificate-based repositories.
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package openmpi.x86_64 0:1.5.4-2.el6 will be installed
--> Processing Dependency: libesmtp.so.5()(64bit) for package: openmpi-1.5.4-2.el6.x86_64
--> Running transaction check
---> Package libesmtp.x86_64 0:1.0.4-15.el6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

================================================================================
 Package
    Arch   Version      Repository                                         Size
================================================================================
Installing:
 openmpi
    x86_64 1.5.4-2.el6  springdale.princeton.edu_data_puias_6.5_x86_64_os 2.2 M
Installing for dependencies:
 libesmtp
    x86_64 1.0.4-15.el6 springdale.princeton.edu_data_puias_6.5_x86_64_os  57 k

Transaction Summary
================================================================================
Install       2 Package(s)

Total size: 2.3 M
Installed size: 7.5 M
Is this ok [y/N]: y
Downloading Packages:
warning: rpmts_HdrFromFdno: Header V3 RSA/SHA256 Signature, key ID 41a40948: NOKEY


Public key for openmpi-1.5.4-2.el6.x86_64.rpm is not installed

Any idea how this could be sorted? There's really no point in working with clusters if no parallelisation is possible..!
Same happens with openmpi-devel.

I have also installed paraview by manually downloading the rpm file and installing it through terminals (just like OpenFOAM itself). However, whenever I try to use paraFoam, it says:

FATAL ERROR: ParaView reader module libraries do not exist

Please build the reader module before continuing:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
./Allwclean
./Allwmake

And if I try to re-install it, it says that paraview has already been installed:

sudo rpm -i OpenFOAM-ParaView-3.12.0-1.x86_64.rpm 
        package OpenFOAM-ParaView-3.12.0-1.x86_64 is already installed

Thank you very much for your help

Originally Posted by wyldckat

Greetings jyang1 and welcome to posting on the forum!

As the wiki page you indicated, it briefly explains: https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL


If you look for CentOS at wikipedia, you'll find this description: https://en.wikipedia.org/wiki/CentOS


You probably cannot install the RPM packages from the command line because the network connection you're using relies on a proxy server, which the browser is already configured to work with, but the RPM infrastructure isn't configured to do so. After downloading the files, you can run the rpm command directly with the files you've downloaded, e.g.:

sudo rpm -i OpenFOAM-scotch-6.0.0-1.x86_64.rpm

If using the RPM packages still doesn't work, then are you able to use with success the steps #1 and #2 from these instructions: https://openfoamwiki.net/index.php/I...HEL#CentOS_6.6 - It's for OpenFOAM 2.4.0 and CentOS 6.6, but those two steps should be identical for any CentOS and RHEL 6.x versions. Those steps will install the necessary packages that are needed for building OpenFOAM and ParaView from source code.
If you're able to install the packages stated in step #2, then you can follow the remaining instructions; and whenever it tells you to use "wget" (it's for downloading files from the command line), you should download the file manually.



If you cannot install those packages yourself, then ask your systems administrator.

If the administrator cannot install those packages, the only other 2 ways that I know of:

1. One way is probably to resort to installing CentOS 6.2 in a virtual machine and building OpenFOAM inside the virtual machine. Once the build is complete, you can transfer it to the real machine that has RHEL 6.2.
   • You can find instructions on how to transfer the installation from the virtual machine to the real machine here: http://www.cfd-online.com/Forums/ope...tml#post525535 - post #5
2. Another is to use the pre-built versions provided by the CentFOAM project: http://sourceforge.net/projects/centfoam/ - the closest installation instructions I could find right now are these: http://www.cfd-online.com/Forums/ope...tml#post362913

Best regards,Bruno

[wyldckat]

Hi jyang1,

Looks like you need to disable the repository that is giving this problem. It seems that the repository was added when you tried following the instructions for installing in RHEL from source code: http://www.openfoam.org/archive/2.3....oad/source.php

Therefore, try running the following commands for disabling the two repositories that were added:

yum-config-manager --disable springdale.princeton.edu\*

Then try installing Open-MPI and the 'Development Tools' again.

As for the problem with ParaView, it might because the OpenFOAM shell environment needs to be updated. For example, start a new terminal and run:

source /opt/OpenFOAM-2.3.0/etc/bashrc

Best regards,
Bruno

[jyang1]

[/QUOTE]Hi wyldckat,

Thank you for your reply.

I've followed your commands and I get the following messages:

[root@nodemaster01 ~]# yum-config-manager --disable springdale.princeton.edu\*

Loaded plugins: product-id, refresh-packagekit
========================================================================================================== repo: springdale.princeton.edu_data_puias_6.5_x86_64_os ===========================================================================================================
[springdale.princeton.edu_data_puias_6.5_x86_64_os]
bandwidth = 0
base_persistdir = /var/lib/yum/repos/x86_64/6Server
baseurl = http://springdale.princeton.edu/data/puias/6.5/x86_64/os
cache = 0
cachedir = /var/cache/yum/x86_64/6Server/springdale.princeton.edu_data_puias_6.5_x86_64_os
cost = 1000
enabled = False
enablegroups = True
exclude = 
failovermethod = priority
gpgcadir = /var/lib/yum/repos/x86_64/6Server/springdale.princeton.edu_data_puias_6.5_x86_64_os/gpgcadir
gpgcakey = 
gpgcheck = True
gpgdir = /var/lib/yum/repos/x86_64/6Server/springdale.princeton.edu_data_puias_6.5_x86_64_os/gpgdir
gpgkey = 
hdrdir = /var/cache/yum/x86_64/6Server/springdale.princeton.edu_data_puias_6.5_x86_64_os/headers
http_caching = all
includepkgs = 
keepalive = True
mdpolicy = group:primary
mediaid = 
metadata_expire = 21600
metalink = 
mirrorlist = 
mirrorlist_expire = 86400
name = added from: http://springdale.princeton.edu/data/puias/6.5/x86_64/os
password = 
persistdir = /var/lib/yum/repos/x86_64/6Server/springdale.princeton.edu_data_puias_6.5_x86_64_os
pkgdir = /var/cache/yum/x86_64/6Server/springdale.princeton.edu_data_puias_6.5_x86_64_os/packages
proxy = 
proxy_dict = 
proxy_password = 
proxy_username = 
repo_gpgcheck = False
retries = 10
skip_if_unavailable = False
sslcacert = 
sslclientcert = 
sslclientkey = 
sslverify = True
throttle = 0
timeout = 30.0
username = 

====================================================================================================== repo: springdale.princeton.edu_data_puias_DevToolset_6.5_x86_64 =======================================================================================================
[springdale.princeton.edu_data_puias_DevToolset_6.5_x86_64]
bandwidth = 0
base_persistdir = /var/lib/yum/repos/x86_64/6Server
baseurl = http://springdale.princeton.edu/data/puias/DevToolset/6.5/x86_64
cache = 0
cachedir = /var/cache/yum/x86_64/6Server/springdale.princeton.edu_data_puias_DevToolset_6.5_x86_64
cost = 1000
enabled = False
enablegroups = True
exclude = 
failovermethod = priority
gpgcadir = /var/lib/yum/repos/x86_64/6Server/springdale.princeton.edu_data_puias_DevToolset_6.5_x86_64/gpgcadir
gpgcakey = 
gpgcheck = True
gpgdir = /var/lib/yum/repos/x86_64/6Server/springdale.princeton.edu_data_puias_DevToolset_6.5_x86_64/gpgdir
gpgkey = 
hdrdir = /var/cache/yum/x86_64/6Server/springdale.princeton.edu_data_puias_DevToolset_6.5_x86_64/headers
http_caching = all
includepkgs = 
keepalive = True
mdpolicy = group:primary
mediaid = 
metadata_expire = 21600
metalink = 
mirrorlist = 
mirrorlist_expire = 86400
name = added from: http://springdale.princeton.edu/data/puias/DevToolset/6.5/x86_64
password = 
persistdir = /var/lib/yum/repos/x86_64/6Server/springdale.princeton.edu_data_puias_DevToolset_6.5_x86_64
pkgdir = /var/cache/yum/x86_64/6Server/springdale.princeton.edu_data_puias_DevToolset_6.5_x86_64/packages
proxy = 
proxy_dict = 
proxy_password = 
proxy_username = 
repo_gpgcheck = False
retries = 10
skip_if_unavailable = False
sslcacert = 
sslclientcert = 
sslclientkey = 
sslverify = True
throttle = 0
timeout = 30.0
username =

Then if I try to install Development Tools and Openmpi,

[root@nodemaster01 ~]# sudo yum install 'Development Tools'

Loaded plugins: product-id, refresh-packagekit, security, subscription-manager
Updating certificate-based repositories.
Setting up Install Process
No package Development Tools available.
Error: Nothing to do

[root@nodemaster01 ~]# sudo yum install openmpi openmpi-devel qt zlib-devel cmake

Loaded plugins: product-id, refresh-packagekit, security, subscription-manager
Updating certificate-based repositories.
Setting up Install Process
No package openmpi available.
No package openmpi-devel available.
Nothing to do

I checked my mpi version just in case and I get the following message:

[root@nodemaster01 ~]# mpirun --version
mpirun (Open MPI) 1.6.5

Report bugs to http://www.open-mpi.org/community/help/

Just in case it helps you in any way, the working order I followed to install OF was: 1. terminal update 2. install development tools and any relevant packages such as openmpi (which doesn't seem to be done correctly) 3. manually download OF and paraview rpm files and install them. So considering the development tools had been installed before installing rpm files, perhaps it's not problems caused by repositories?

When I try to run in parallel, I get the following error message

[root@nodemaster01 trial]# mpirun -np 4 icoFoam
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  opal_shmem_base_select failed
  --> Returned value -1 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
[nodemaster01:06623] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file runtime/orte_init.c at line 79
[nodemaster01:06623] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file orterun.c at line 694

Also, regarding paraview, updating the OpenFOAM shell environment doesn't seem to be fixing the problem (or I may be doing it wrong).
Your command couldn't find the correct directory, so I changed it a bit, but I am not sure if this is the right directory you intended to update

[root@nodemaster01 ~]# ls
Abaqus_6.14-1_InstallLog.log    fftw-2.1.5             Music
abaqus_lic                      fftw-2.1.5.tar.gz      OpenFOAM
abaqus_plugins                  fftw-3.3.3.tar.gz      OpenFOAM-2.3.x
abaqus.rpy                      GC262_0513             opt_intelv12.tar.gz
abaqus.rpy.1                    GC2_install_cent64.sh  Pictures
abaqus_v6.14.gpr                hack                   Public
anaconda-ks.cfg                 ifcfg-wlan0            rhel_check.log
app_enhpc_intel12_rhel6.tar.gz  install.log            _STEP_R.log
Desktop                         install.log.syslog     _STEP_W.log
Documents                       lammps_stable.tar.gz   Templates
Downloads                       ll.log                 Videos

[root@nodemaster01 ~]# pwd
/root
[root@nodemaster01 ~]# source /root/OpenFOAM/OpenFOAM-2.3.x/etc/bashrc

[root@nodemaster01 ~]# cd OpenFOAM/root-2.3.x/run/tutorials/incompressible/icoFo
am/cavity/

[root@nodemaster01 cavity]# paraFoam 

FATAL ERROR: ParaView reader module libraries do not exist

Please build the reader module before continuing:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
./Allwclean
./Allwmake

(if you notice, there are two openfoam directories in the root directory. Please note that the folder "OpenFOAM" is the one I am using, not the "OpenFOAM-2.3.x", although there is effectively another "OpenFOAM-2.3.x" folder within the "OpenFOAM" folder)


What could be causing the problems?

Thank you kindly

Originally Posted by wyldckat

Hi jyang1,

Looks like you need to disable the repository that is giving this problem. It seems that the repository was added when you tried following the instructions for installing in RHEL from source code: http://www.openfoam.org/archive/2.3....oad/source.php

Therefore, try running the following commands for disabling the two repositories that were added:

yum-config-manager --disable springdale.princeton.edu\*

Then try installing Open-MPI and the 'Development Tools' again.

As for the problem with ParaView, it might because the OpenFOAM shell environment needs to be updated. For example, start a new terminal and run:

source /opt/OpenFOAM-2.3.0/etc/bashrc

Best regards,
Bruno

[wyldckat]

Hi jyang1,

OK, let's see if I don't get lost in addressing each issue...

The first "problem" is that you no longer have any repository enabled for working with yum. Apparently you only had two repositories that were turned on:

• springdale.princeton.edu_data_puias_6.5_x86_64_os
• springdale.princeton.edu_data_puias_DevToolset_6.5 _x86_64

By running the command I suggested, these two were turned off as well. The problem is that the instructions provided at http://www.openfoam.org/archive/2.3....oad/source.php assume that the original repositories are working as intended in order for these two commands to work:

yum groupinstall 'Development Tools'
yum install openmpi openmpi-devel

For solving this issue, I would suggest contacting your system's administrator, in order to know if you can turn back on the original repositories your system used for RHEL 6.2, in order to install some of the missing packages.


Now, if you were able to install the RPM package "OpenFOAM-2.3.0-1.x86_64.rpm", then that means that OpenFOAM is installed in this folder:

/opt/OpenFOAM-2.3.0

But you apparently also have another installation, namely 2.3.x. This is a problem... what I mean is that you're mixing various version of OpenFOAM without taking the appropriate steps for setting up each version. In addition, it seems that you have OpenFOAM 2.3.x installed as root in the root folder, which is a very bad idea... in the sense that you're taking a risk and that you might accidentally end up damaging your main system installation due to an accidental file/folder deletion.


The Open-MPI version 1.6.5 that you have probably is one that is part of the OpenFOAM 2.3.x installation. As to why it's not working... it probably is related to the confusion in the various installed versions of OpenFOAM.


The ParaView version installed with the RPM package "OpenFOAM-ParaView-3.12.0-1.x86_64.rpm" was specifically designed to work with the respective OpenFOAM 2.3.0 RPM package. Technically you can still use it with 2.3.x, but you will have to run paraFoam like this:

paraFoam -builtin

In order to properly fix all of this confusion, I suggest that you first decide what specific version of OpenFOAM you want to use.

Best regards,
Bruno