## Abaqus installation problems on 64 bit Linux

April 14th, 2008 | Categories: applications, Linux | Tags:

Abaqus is an extremely powerful finite element analysis (FEA) package that is used by various departments at my university and it is an application that I provide some of the support for among our users. I am far from being an expert at using it but I do know a trick or two and am occasionally useful. Recently, someone emailed me because they were having trouble actually getting Abaqus 6.6 installed on a 64 bit CENTOS 5 machine. He was located on the other side of campus from me, but it was a nice day and I felt like a walk so, rather than giving the support via email, I popped over to see him face to face. I am glad I did too – because it was a tricky one!

I am aware that this is not the sort of thing my usual readers might be interested in so I will keep it as brief as possible – basically what I want to do is provide myself with a permanent record of what we discovered and how we fixed it in case I come across this problem again. In an ideal world it might also help a googler or two (do let me know in the comments if it does – it will make my day)

So…we log on as root, run the installation script and get the following error

Extracting temporary installation utilities to /opt/temp…
Executing the installation GUI…
Preparing to install…
Extracting the installation resources from the installer archive…
Configuring the installer for this system’s environment…
awk: error while loading shared libraries: libdl.so.2: cannot open shared object file: No such file or directory
dirname: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
/bin/ls: error while loading shared libraries: librt.so.1: cannot open shared object file: No such file or directory
basename: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
dirname: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
basename: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
hostname: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory

Launching installer…
grep: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
/opt/temp/TEMP_ABAQUS_utils_root/jre/bin/java: error while loading shared libraries: libpthread.so.0: cannot open shared object file: No such file or directory

As far as I can tell the reason for this is that the installer cannot identify your shiny new kernel so it assumes that an old one is being used and THIS is where the problems start. The problem occurs in the script /cdrom/lnx86_64/product/UNIX/Disk1/InstData/NoVM/install.bin

Look inside this file and you will see 2 lines that contain

export LD_ASSUME_KERNEL

I commented these out by adding a # (after copying the installation cd to a writable filesystem of course):

#export LD_ASSUME_KERNEL

BIG mistake. I now had a shiny new error

Exception in thread "main" java.lang.NoClassDefFoundError: com/zerog/lax/LAX

After a bit of googling, I discovered this post which gave an explanation of the problem along with a solution. The important part is this:

“make sure any line you put a comment on, you either edit in overwrite mode, or you make sure you delete a character for every # sign you add”

I deleted the Tab character before each of the # I had added and the error went away but I could have saved myself the grief by NOT manually commenting out each instance of LD_ASSUME_KERNEL and just running the following sed command on install.bin instead

cat install.bin | sed “s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/” > /tmp/install.bin

Once this was taken care of, the installation proceeded without complaint and I was pretty confident that I was going to be out in time to meet my friend for coffee but, alas, it was not to be. When I tested the install by running the abaqus cae I received the following error message

I was starting to contemplate writing some FEA code for him rather than continue with this install as I felt that it might have been easier but it turned out that all we need to do is change the name of a couple of files (original source here). Do the following at your shell prompt (assuming the default installation location):

cd /opt/abaqus/6.6-1/External
mv libgcc_s.so libgcc_s.so.BACKUP
mv libgcc_s.so.1 libgcc_s.so.1.BACKUP

Job done! Finally! As always, if anyone finds this useful then please let me know.

1. It has saved my life when I was installing Abaqus 6.6 – thanks a lot.
By the way-recently I was installing Abaqus 6.7 and I have not met this problem.

Warsaw University of Technology
Poland

2. Thank you very much for such a useful post. Probably you have save me
from mental disease… and also a computational cluster to be thrown
through a window.

Daniel Esqué de los Ojos
Department of Fluid Mechanics
Universitat Politècnica de Catalunya
EU Enginyers Tècnics Industrials de Barcelona
Comte Urgell 187
08036 Barcelona

3. When I tried to install ABAQUS 6.11 on my LINUX 64 bit (RHEL 5.4) hpc server I got the error Java Virtual Machine not installed can you please guide me what is missing

Dr. C.S. Pathak
Professor of Mechanical Engineering