Re: Issue With CatDCD in Dynamical Network Tutorial

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Mon Jul 15 2019 - 09:45:04 CDT

Hello Collin,

You don't need to compile a precompiled binary. chmod +x catdcd and then adding to $PATH (which you did) is suffice.

You need to install libstdc++6. The error message is quite obvious:

error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory

On Wed, Jul 10, 2019 at 4:50 PM Nisler, Collin R. <nisler.1_at_buckeyemail.osu.edu<mailto:nisler.1_at_buckeyemail.osu.edu>> wrote:

Hello, I was recently trying to do the Dynamical Network Analysis tutorial, and I ran into an issue with catdcd. In the tutorial, it indicates that you need to download the precompiled CatDCD binary. On the website where the files are located (http://www.ks.uiuc.edu/Development/MDTools/catdcd/) it indicates that, once it is unpacked, you need to run the makefile in the "catdcd" directory. However, there is no makefile after unpacking, and I believe this is why I am encountering an error in the tutorial. When I run the command "networkSetup network.config" in the TK console, as instructed in the tutorial, it says that catdcd was not found (even though I added it to my path as instructed in the tutorial) and asks if I want to specify the path. When I specify the path of the binary, I get the following error in the TK console:


-code 1 -level 0 -errorcode {CHILDSTATUS 27684 127} -errorinfo {/home/cbc-sotomayor-labhome4/nisler.1/Catdcd/LINUX/bin/catdcd4.0/catdcd: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory
    while executing
"::exec /home/cbc-sotomayor-labhome4/nisler.1/Catdcd/LINUX/bin/catdcd4.0/catdcd -stride 1 -i carma.indices -o carma.dcd ../../../../../AncAmP15C23-mine..."
    ("eval" body line 1)
    invoked from within
"eval ::exec [list $exec_path] [lrange $args 1 end]"
    (procedure "::ExecTool::exec" line 14)
    invoked from within
"::ExecTool::exec catdcd -stride $stride -i $indexFile -o $outFile $dcdFileNames"
    ("eval" body line 1)
    invoked from within
"eval ::ExecTool::exec {catdcd -stride $stride -i $indexFile -o $outFile $dcdFileNames} "} -errorline 13


I have also tried using the catdcd from the VMD plugin tree, but that does not work either. I am using VMD 1.9.3. Any help would be greatly appreciated.


Collin Nisler

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