[modeller_usage] segfault writing alignment file

["Meesters, Christian" <>]

Hi,

I'm using modeller v9.9 in a Linux environment (Ubuntu 11.04) with Python 2.7. When running a script like the build_profile.py from the tutorial, everything works fine, except for the last line:

aln.write(file='build_profile.ali', alignment_format='PIR')

which results in:

openf___224_> Open           build_profile.ali
Segmentation fault

The file is created, but nothing gets written to it.

Writing to Python file objects with a simple

x = open('test', 'w')
x.write('test')
x.close()

works. So I dare to conclude this is no permissions thing.

Although running modeller only via Python, I thought perhaps this is of interest, too:

$ ldd mod9.9_x86_64-intel8
        linux-vdso.so.1 =>  (0x00007fff643ff000)
        libmodeller.so.5 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libmodeller.so.5 (0x00007f709af77000)
        libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f709ac62000)
        libpython2.3.so.1.0 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libpython2.3.so.1.0 (0x00007f709aa37000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f709a6a3000)
        libifcore.so.5 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libifcore.so.5 (0x00007f709a493000)
        libsvml.so => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libsvml.so (0x00007f709a308000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f709a104000)
        libhdf5.so.6 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libhdf5.so.6 (0x00007f7099c69000)
        libhdf5_hl.so.6 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libhdf5_hl.so.6 (0x00007f7099a3d000)
        libsaxs.so => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libsaxs.so (0x00007f709983c000)
        libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f70995ff000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f70993f7000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f70991d9000)
        libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f7098fd5000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f7098d50000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f709b52b000)
        libimf.so => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libimf.so (0x00007f70989ec000)
        libintlc.so.5 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libintlc.so.5 (0x00007f70988ae000)

So, no missing libraries, but perhaps a wrong version?

Any ideas on what might trigger this segfault?

TIA
Christian