Installing on Ubuntu Server 16.04 LTS

[Björklund]

Hi,

So, A colleague and I have tried installing Elegant and Pelegant on Ubuntu Server 16.04 LTS, and we don't quite get it to work, in spite of following the guide.

To begin with, we used the pre-built rpm for the SDDS toolbox and Elegant, which allowed us to start Elegant. However, any attempt to run example files ended with SIGSEGVProgram trace-back. After this, after removing the previous elegant installation, we tried building the RPMs ourselves using theBuild-AOP-RPMs script. Everything seems fine when running the script, no errors (but some warning regarding language and time format or so), but there is no folder created containing the RPMs - the only folder that's created is the oagsoftware folder with SDDS and Epics.

We're pretty much stuck here, so I thought it'd be a good idea to ask for help.

Best regards
Jonas

[soliday]

I'm going to run some tests on ubuntu 16.04 to check it. As for the script to build the RPMs, it sounds like it is failing somehow. The oagsoftware directory is supposed to be deleted at the end. The RPM files will be in the rpmbuild directory.

[Björklund]

Hi,

So, the RPM directory is nowhere to be found. There was another thing I forgot to mention, which might or might not be important, which is that when we run elegant, it says that the SVN revision is unknown. I don't remember seeing this before (not that I looked for it, though), so I thought I'd mention it.

Thanks for looking into it!
//Jonas

[soliday]

I tried a few example files and they completed properly. Is there a specific one that doesn't work?

What do you get when you run ldd on the elegant executable? I'd like to see if you are using different system libraries than me.

$ ldd /usr/bin/elegant
linux-vdso.so.1 => (0x00007ffecf727000)
libgsl.so.19 => /usr/lib/x86_64-linux-gnu/libgsl.so.19 (0x00007f3cf6d2d000)
libgslcblas.so.0 => /usr/lib/x86_64-linux-gnu/libgslcblas.so.0 (0x00007f3cf6aef000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f3cf68d4000)
liblapack.so.3 => /usr/lib/liblapack.so.3 (0x00007f3cf60dc000)
libblas.so.3 => /usr/lib/libblas.so.3 (0x00007f3cf5e6d000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f3cf5c4f000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f3cf5946000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f3cf557c000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007f3cf5250000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f3cf503a000)
/lib64/ld-linux-x86-64.so.2 (0x00005620275dc000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f3cf4dfa000)

If you are not executing Build-AOP-RPMs with sudo, then you have to ensure that you already have all the development system libraries installed. These include: wget subversion gzip tar make rpm alien gcc g++ gfortran zlib1g-dev libgd2-xpm-dev liblapack-dev libblas-dev libxaw7-dev libncurses5-dev libxt-dev tcl-dev tk-dev csh python-dev python3-dev unzip libpng12-dev libgsl-dev libmotif-dev libtiff5-dev libreadline5-dev libhdf5-serial-dev

[Björklund]

Hi,

So, this is what I get when I run "ldd /usr/bin/elegant":
ldd /usr/bin/elegant
linux-vdso.so.1 => (0x00007ffee7915000)
libgsl.so.19 => /usr/lib/x86_64-linux-gnu/libgsl.so.19 (0x00007fe7b99f7000)
libgslcblas.so.0 => /usr/lib/x86_64-linux-gnu/libgslcblas.so.0 (0x00007fe7b97b9000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fe7b959f000)
liblapack.so.3 => /usr/lib/liblapack.so.3 (0x00007fe7b8dbc000)
libblas.so.3 => /usr/lib/libblas.so.3 (0x00007fe7b8b5b000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fe7b893e000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fe7b8635000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fe7b826b000)
libopenblas.so.0 => /usr/lib/libopenblas.so.0 (0x00007fe7b61d7000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007fe7b5eac000)
/lib64/ld-linux-x86-64.so.2 (0x00007fe7b9e36000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007fe7b5c6d000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fe7b5a57000)

I ran the Build-AOP-RPMs script with sudo and it worked this time. I thought we did that the first time, but apparently not. I installed elegant and the SDDS toolbox via the rpm directory that was created now.

Let me know if everything looks all right there. I still cannot run example files, program is still killed by SIGSEGVPogram trace-back.

//Jonas

[soliday]

I don't see anything obvious. Your build is linking to libopenblas which I am unfamiliar with but I doubt that is the problem.

Try running elegant inside gdb. As an example go to examples/matching/betaMatching and run:
gdb elegant
gdb> run one.ele
gdb> where
gdb> list

This should help us understand where it is crashing.

[Björklund]

Hi,

I put the output of your suggested commands in the attached .txt file, the output was a bit long to post directly in the thread. Towards the end of the output, there is a file that the program doesn't find, fprintf_chk.c.

//Jonas

[soliday]

When you run "rpn" from the commandline do you get the same error message? rpn is included with the SDDSToolKit RPM.

I think something is wrong with your defns.rpn file. Can you re-download it from http://ops.aps.anl.gov/downloads/defns.rpn and set the RPN_DEFNS environment variable to point to this file?

It should be 6622 bites in size if downloaded correctly.

[Björklund]

Hi,

When I run rpn I get

elegantExamples/examples/matching/betaMatching$ rpn
Welcome to rpn version 6, by Michael Borland and Robert Soliday (June 1999).
Segmentation fault (core dumped)

so something seems off. I'll try to set the file again and I'll report back.

//Jonas

[Björklund]

Hi,

Ok, so now I managed to run the one.ele file in the beta matching directory! The rpn files looked the same at a quick glance, but the first one must have been faulty in some way.

I'll write if something else pops up.

Thanks so much for the help and have a nice weekend!

//Jonas