VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Mar 21 2016 - 09:08:04 CDT

Hi Laura,

Ahh, ok. Would you mind posting the section of the script that's doing
the atomselection? Preferably the whole function, if possible. What I
suspect what is going on is that an atomselection is being made inside a
loop, and isn't deleted. VMD has to allocate memory for every
atomselection, and does not release the allocation unless the
atomselection is explicitly deleted. You might have a longer trajectory
or a larger system than the person who wrote the script, so you are
running into problems they did not. Again, with a script in hand, its
alot easier to assess what is going on.

-Josh Vermaass

On 03/21/2016 08:44 AM, Laura Joana wrote:
> Hello Josh,
>
> I think you are right! In fact "mol new 1DV3" works perfectly! So I'm
> new in VMD and the script was not written by me and theoretically it
> should work. So I commented a few lines and I discovered the problem
> is with the line that calls the atomselect function. Maybe it's a
> memory problem, but I have no idea how to confirme that! All I know is
> that I get segmentation fault....
>
> 2016-03-18 19:42 GMT+01:00 Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>>:
>
> Hi Laura,
>
> rlwrap is likely not at fault here. You say that VMD runs, right?
> That means you can load a simple pdb file directly right? I get
> these rlwrap warnings on ubuntu too, but usually when I do
> something silly like run my computer out of memory so that VMD is
> forced to crash. What is the tcl script supposed to do? That is
> the part I'd start investigating. If a simple command like: "mol
> new 1DV3" works, it points the finger at the script doing
> something that will run you out of memory without meaning to.
>
> -Josh Vermaas
>
>
> On 03/18/2016 10:37 AM, Laura Joana wrote:
>> Dear all,
>>
>> I installed locally the last version of VMD (text-mode) and I got
>> this error after running the vmd command:
>> rlwrap: No match.
>> I found other users talking about that bug:
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19158.html
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_mailing-5Flist_vmd-2Dl_19158.html&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=l4Hd_IVgbDUmCECCICCeDyqRRSs1jICo0ThoYSvD3sA&s=s3HvcquGDmkhunKhd4S5laYzXJQ1F2o-MjGrKG-7YVE&e=>
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/24032.html
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_mailing-5Flist_vmd-2Dl_24032.html&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=l4Hd_IVgbDUmCECCICCeDyqRRSs1jICo0ThoYSvD3sA&s=KqeLVToccU0vXrnuHXIEnatBSyz1xIZNAackvWUF99o&e=>
>> The first one recommends to take off all the symbols from the
>> rlwrap command line. The second one recommends taking just the
>> "[" character off, and maybe changing the shell. I tried all of
>> this and vmd runs, but, when I try to read a tcl script using the
>> source command I get this:
>>
>> rlwrap: warning: vmd killed by SIGSEGV (core dumped).
>> rlwrap has not crashed, but for transparency,
>> it will now kill itself with the same signal
>>
>> Segmentation fault (core dumped)
>>
>> In this site:
>> http://askubuntu.com/questions/221135/issue-with-vmd-install-not-working-any-more-lubuntu-12-10
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__askubuntu.com_questions_221135_issue-2Dwith-2Dvmd-2Dinstall-2Dnot-2Dworking-2Dany-2Dmore-2Dlubuntu-2D12-2D10&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=l4Hd_IVgbDUmCECCICCeDyqRRSs1jICo0ThoYSvD3sA&s=yQxZrAFrov6M-KMZ4Q3tf1xPBMItqSRgvmY8VsLgU4w&e=>
>> they recommend to uninstall rlwrap. As I can not do that (because
>> I'm in a lab cluster) I set the variable $rlwrap empty. I got just:
>> Segmentation fault (core dumped)
>> after I tried to run my tcl script.
>>
>> It seems that the problem is really with rlwrap, but I have o
>> clue to resolve this. Does someone here knows how to fix this?
>>
>> Thanks
>>
>> Laura
>>
>
>