ATSAS 2.7.1 on ubuntu 15.10

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galaad112
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ATSAS 2.7.1 on ubuntu 15.10

#1 Post by galaad112 » 2016.02.25 22:40

Dear,

I used without problem atsas 2.7.1 on ubuntu 15.10 but since a recent update I have this error message : eom: /usr/lib/x86_64-linux-gnu/atsas/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/lib/x86_64-linux-gnu/libicuuc.so.55)



I tried to reinstall it many times, to reinstall libraries concerned by this problem, to change the library source but without any success. Could you help me with this problem?


Thanks a lot

A SAXS User

Juan
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Joined: 2016.08.05 14:02

Re: ATSAS 2.7.1 on ubuntu 15.10

#2 Post by Juan » 2016.08.05 15:01

I had the same problem after installing ATSAS-2.7.2-5_amd64.deb on Ubuntu 16.04 LTS. Strangely enough, the library in /usr/lib/x86_64-linux-gnu/atsas/ is the culprit, while ATSAS programs can be executed using the one from a different location (/usr/lib/x86_64-linux-gnu/libstdc++.so.6 in my case).

I found in stackoverflow.com a way to force the use of the second library by using LD_PRELOAD. For example, in my case I would run eom as:

Code: Select all

LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 eom
However I would like to ask the experts if there is a way of linking all ATSAS programs to this library without having to make an alias for each and, more importantly, whether this is a valid solution to begin with (both libstdc++.so.6 files have very different sizes).

MikeR
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Joined: 2016.08.31 22:43

Re: ATSAS 2.7.1 on ubuntu 15.10

#3 Post by MikeR » 2016.08.31 22:57

I ran into a similar problem with Ubuntu 16.04 and solved it by reversing the order of the LD_LIBRARY_PATH search so that it went through the system supplied libraries first. The setup follows:

ATSAS=/usr/local/src/atsas/ATSAS-2.7.2-5
export ATSAS
PATH=$ATSAS/bin:$PATH
export PATH
LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/:$ATSAS/lib/x86_64-linux-gnu/atsas/
export LD_LIBRARY_PATH

This eliminated all of the run-time errors that I encountered.

I hope it is helpful.

Juan
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Posts: 2
Joined: 2016.08.05 14:02

Re: ATSAS 2.7.1 on ubuntu 15.10

#4 Post by Juan » 2016.09.02 14:39

Given my lack of Linux skills I had just replaced the library supplied by ATSAS with the one from the system (after making a backup copy), but your method certainly looks better.

I just wanted to point out that running ATSAS with this library gives results that are consistent with those from a different computer, so the workaround seems safe.

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