[Cod-bugs] Trouble installing COD-Tools on a supercomputer

[Andrius Merkys]

Hi Ray,

I seem to understand the issue. Scripts build.sh and run.sh, located in dependencies/, are used only to install dependencies for specific OSes, building of the package is done via 'make'. Apparently, you have used a build.sh script intended for Debian, hence the 'apt-get'. There is a script for CentOS 6.8 in dependencies/CentOS-6.8/ using yum package manager, I think this one is the closest to RHEL. Be sure to use both build.sh and run.sh:

source dependencies/CentOS-6.8/build.sh
source dependencies/CentOS-6.8/run.sh
make
make install PREFIX=/usr/local # or any other location

Best,
Andrius

On 04/27/2018 10:08 AM, Ray Sheppard wrote:
> Hi Andreas,
>   Thanks for the reply.  We have two systems.  The Cray's CLE is pretty daunting, so I am trying on the simpler RHEL6 and 7 cluster.
> My first trouble comes in the very first line of build.sh:
> sudo apt-get install -y
> The script can not have sudo.  Then come the long list of prereqs.  I am unsure of the specialty perls, but I already have a bison, flex, gcc, perl, python, python-dev and swig it can see. Poking around in the package, it looked like the various pieces were stashed in the tarfile.  So I thought it was going to "install" them.  Removing sudo results in "apt-get: command not found"  At this point I was lost and thought I should ask for help.
>       Ray
>
> On 4/27/2018 2:49 AM, Andrius Merkys wrote:
>> Dear Roy,
>>
>> thank you for your message. However, I need clarification concerning some points of it. Building cod-tools from source does not perform compilation of any of its dependencies (Perl, bison and gcc), our software is designed to use programs and libraries already installed either in standard locations or pointed to environment variables PATH (for executables) and PERL5LIB (for Perl libraries), which are usually set up using modules (I assume you mean using Modules package, https://linux.die.net/man/1/module, am I right?). Once you build the cod-tools no compilation should be required any more.
>>
>> We could, in principle, provide pre-compiled packages, but currently we have not enough resources to cover all possible architectures. If you are using Debian, you may use our Debian package repository (http://wiki.crystallography.net/debian_package_repository/ describes how to use it), we already cover amd64 and armhf architectures for Debian 8.
>>
>> Please let us know should you need more help.
>> Best,
>> Andrius
>>
>> On 04/27/2018 02:10 AM, Ray Sheppard wrote:
>>> Hello,
>>>    I am not actually reporting a bug.  Your package has been
>>> successfully built on a workstation.  This was just the only contact e-mail address I could locate.
>>>
>>>    We have received a request from our Electron Microscopy Center to
>>> install COD_Tools for them on our supercomputers so they do not have to
>>> offload their data to a local system.  However, I have run into
>>> troubles.  The build shells seem preoccupied with building packages like
>>> Perl, Bison GCC and others themselves.  These already exist on our
>>> machines. They exist in non-standalone locations and their environments
>>> are loaded using modules.  What would be really helpful would be the
>>> package to compile and just use the prerequisites it needs from its
>>> environment.  Of course, it also will be put in a different file system
>>> and no scripts have the rights to sudo.  Any direction you could give,
>>> would be very helpful.
>>> Thank you,
>>>    Ray Sheppard
>>>
>>>   Advanced Parallel Applications
>>>   Science Community Tools
>>>   Research Technologies
>>>   UITS
>>>   Indiana University
>>>
>>> _______________________________________________
>>> Cod-bugs mailing list
>>> Cod-bugs at lists.crystallography.net
>>> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania