QuantumATK Forum
QuantumATK => Installation and License Questions => Topic started by: Dipankar Saha on December 10, 2013, 16:01
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What is meaning of this error message????
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/usr/local/QuantumWise_13/atk-13.8.0/atkpython/bin/atkpython: line 7: 28894 Segmentation fault (core dumped) $EXEC_DIR/atkpython_exec $*
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I'm fairly sure your calculation is trying to use more memory than is available on the computer.
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We did a small experiment to test this, we upgraded a system running RHEL 6.3 to RHEL 6.5.
ATK 13.8.0 was running perfectly with RHEL 6.3 but upon upgradation to RHEL 6.5 ATK is showing the segmentation fault mentioned above.
So we strongly believe that ATK 13.8 is not compatible to RHEL 6.5, kindly fix this bug ASAP.
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Can you run a small test calculation on RHEL 6.5, just a 1 atom system? Things related to compatibility are pretty binary - either it works (for any size system) or it doesn't. But since I don't know if your original calculation was a huge system or not, I need more information. Also - does VNL start up?
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VNL does start up but after submitting the job it gives segmentation error, irrespective of the size of the structure. We would like to add that in a new machine we made a fresh install of RHEL 6.5 and after installing ATK 13.8.0 in it, it shows the same problem.
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Is there a "crashlog.txt" file in the directory you start in?
Can you try
cd ATK_INSTALL_DIR (replace with actual install dir - the directory with subdirs "atkpython", "vnl", etc)
ldd atkpython/bin/atkpython_exec
ldd vnl/bin/vnl_exec
LD_LIBRARY_PATH=atkpython/lib ldd atkpython/lib/python2.7/_NLEngine.so
and let us know the output.
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[root@nano4 QuantumWise_13]# ls
analysis.nc atk.ico doc uninstall version.txt
atk-13.8.0-linux64.bin atkpython license Uninstall Atomistix ToolKit 13.8.0.desktop vnl
[root@nano4 QuantumWise_13]# cd atkpython
[root@nano4 atkpython]# ls
bin examples include lib share
[root@nano4 atkpython]# ldd atkpython/bin/atkpython_exec
ldd: atkpython/bin/atkpython_exec: No such file or directory
[root@nano4 atkpython]# cd ..
[root@nano4 QuantumWise_13]# ldd atkpython/bin/atkpython_exec
linux-vdso.so.1 => (0x00007fff2bdff000)
libpython2.7.so.1.0 => not found
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f855c6b6000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f855c4b2000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007f855c2af000)
libm.so.6 => /lib64/libm.so.6 (0x00007f855c02a000)
libc.so.6 => /lib64/libc.so.6 (0x00007f855bc96000)
/lib64/ld-linux-x86-64.so.2 (0x00007f855c909000)
[root@nano4 QuantumWise_13]# ldd vnl/bin/vnl_exec
linux-vdso.so.1 => (0x00007fff9f78a000)
libpython2.7.so.1.0 => not found
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fbe23c28000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fbe23a24000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007fbe23821000)
libm.so.6 => /lib64/libm.so.6 (0x00007fbe2359c000)
libc.so.6 => /lib64/libc.so.6 (0x00007fbe23208000)
/lib64/ld-linux-x86-64.so.2 (0x00007fbe23e7b000)
[root@nano4 QuantumWise_13]# LD_LIBRARY_PATH=atkpython/lib ldd atkpython/lib/python2.7/_NLEngine.so
ldd: warning: you do not have execution permission for `atkpython/lib/python2.7/_NLEngine.so'
linux-vdso.so.1 => (0x00007fff87d74000)
libsymspg.so.0 => atkpython/lib/libsymspg.so.0 (0x00007fe595369000)
libmkl_intel_lp64.so => atkpython/lib/libmkl_intel_lp64.so (0x00007fe594e6c000)
libmkl_intel_thread.so => atkpython/lib/libmkl_intel_thread.so (0x00007fe593a30000)
libmkl_lapack.so => atkpython/lib/libmkl_lapack.so (0x00007fe592cc9000)
libmkl_core.so => atkpython/lib/libmkl_core.so (0x00007fe592812000)
libiomp5.so => atkpython/lib/libiomp5.so (0x00007fe592634000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe5923e2000)
libRocketFuel2.so => atkpython/lib/libRocketFuel2.so (0x00007fe592048000)
librt.so.1 => /lib64/librt.so.1 (0x00007fe591e40000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00007fe591c19000)
libz.so.1 => /lib64/libz.so.1 (0x00007fe591a03000)
libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00007fe5917b3000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x00007fe591532000)
libGL.so.1 => /usr/lib64/libGL.so.1 (0x00007fe5912d3000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fe590fcd000)
libm.so.6 => /lib64/libm.so.6 (0x00007fe590d48000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fe590b32000)
libc.so.6 => /lib64/libc.so.6 (0x00007fe59079e000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fe590599000)
/lib64/ld-linux-x86-64.so.2 (0x00007fe596552000)
libglapi.so.0 => /usr/lib64/libglapi.so.0 (0x00007fe590374000)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x00007fe590160000)
libXdamage.so.1 => /usr/lib64/libXdamage.so.1 (0x00007fe58ff5e000)
libXfixes.so.3 => /usr/lib64/libXfixes.so.3 (0x00007fe58fd58000)
libX11-xcb.so.1 => /usr/lib64/libX11-xcb.so.1 (0x00007fe58fb56000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x00007fe58f819000)
libxcb-glx.so.0 => /usr/lib64/libxcb-glx.so.0 (0x00007fe58f603000)
libxcb-dri2.so.0 => /usr/lib64/libxcb-dri2.so.0 (0x00007fe58f3fe000)
libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00007fe58f1e0000)
libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1 (0x00007fe58efdb000)
libdrm.so.2 => /usr/lib64/libdrm.so.2 (0x00007fe58edcf000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007fe58ebb0000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x00007fe58e9ac000)
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After going through all these steps...., if I try to run vnl 13.8.0....agin I am getting the same error......sayig,
Traceback (most recent call last):
File "./zipdir/NL/GUI/MainWindow/FileBrowser/FileBrowser.py", line 203, in fileSelectionChanged
AttributeError: 'NoneType' object has no attribute 'isDir'
/usr/local/QuantumWise_13/vnl/bin/vnl: line 8: 15811 Segmentation fault (core dumped) $EXEC_DIR/vnl_exec
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The steps above are not supposed to fix anything, they just provide information.
You say "same error" - but clearly now it's a new error, if VNL will not start up properly, whereas before it was atkpython_exec that failed? What are the precise (very exact) steps to reproduce it (which directory what VNL started in, with what command line, what do you do to trigger the error)?
Maybe you tried to start VNL as root this time? Try running it as a regular user, if this was the case. We'll try to set up our own RH 6.5 machine and test if this is a generic problem.
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With the upgrade of Redhat 6.5 was the SSEL secrurity system reenabled?
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Can you please tell, how should I check that...
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Sir,
1) It is not about running VNL from the root.... We have also tried to run it from any other regular user account....but, the Problem is same....
2) It is not only the case that while we upgraded one of our systems from RHEL 6.3 to 6.5 we faced the problem..... rather in case of the fresh installation (for another server) also, we are having the exactly same problem...... / So, re-enabling might not be the issue....
Please tell us how to overcome this problem....
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There might be a relation to an much older RedHat problem.
http://quantumwise.com/component/content/article/25-installation-issues/117-cannot-restore-segment-prot-after-reloc-permission-denied
You could try this resolution on atkpython.so
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ATK is working fine on RedHat RHEL 6.2 and 6.3 (clean installs) but not on RHEL 6.5 irrespective whether it is an upgrade or a clean install. Kindly check the issue, it may be some sort of incompatability with RHEL 6.5.
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We are looking into it, but early indications is that indeed ATK is not compatible with RHEL / CentOS 6.5. We will of course try to solve this, either by making a new build or find a work-around, but for now it would be best to avoid upgrading if possible.
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Dr. A Blom,
Yes...that's what we did ultimately....Again, got back to RHEL 6.3(/6.2).... Otherwise, running ATK-13.8.0 (nor even, 12.8.*) was not possible..../ Hope at the time of the next release, you might be able to solve this issue... :)
Thanks & Regards__
Dipankar Saha
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We are working hard on a solution for RHEL 6.5 but it's NOT easy. Redhat has really made life very, very difficult for us with some choices they have made in the ABI (application binary interface).
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We have managed to find a temporary work around for this,
so if you want to run ATK or VNL, you will have to set this following environment variable before executing:
LD_PRELOAD="libstdc++.so.6" atkpython my_script.py
or
LD_PRELOAD="libstdc++.so.6" vnl
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We have managed to find a temporary work around for this,
so if you want to run ATK or VNL, you will have to set this following environment variable before executing:
LD_PRELOAD="libstdc++.so.6" atkpython my_script.py
or
LD_PRELOAD="libstdc++.so.6" vnl
I could run ATK calculations on CentOS 6.5. Thank you.
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Dr. Nordland,
Thank you sir...for finding some way out...../ Let me check.... :)
Regards__
Dipankar Saha