[AMBER] Fwd: [ics.uci.edu #33898] Fwd: Amber11 download instructions

From: Lane Votapka <lvotapka100.pointloma.edu>
Date: Tue, 22 Feb 2011 09:30:40 -0800

Dear Amber Users,

I've recently been trying to use sLeap, and unsuccessfully because I keep
recieving segfaults when I use the "addions" command followed by the
"saveamberparm" command.

I've found descriptions of similar problems on the archives and internet,
and they sometimes mention a bugfix for the problem. However the most recent
bugfix page I can find is here:


And it sounds like bugfix number 2 fixes the same problem as mine. However
even after making this bugfix sLeap still results in the same error.

Has anyone run into this problem before and been able to resolve it?

-Lane Votapka

---------- Forwarded message ----------
From: Hans Wunsch via RT <helpdesk.ics.uci.edu>
Date: Fri, Feb 18, 2011 at 5:04 PM
Subject: Re: [ics.uci.edu #33898] Fwd: Amber11 download instructions
To: lvotapka100.pointloma.edu, ramaro.uci.edu

HI Lane,

This is the point in program that sleap segfaults:

rt_sigaction(SIGALRM, {SIG_DFL, [], SA_RESTORER, 0x3c2d6302d0},
{0x40d0d4, [], SA_RESTORER, 0x3c2d6302d0}, 8) = 0
rt_sigaction(SIGTSTP, {SIG_DFL, [], SA_RESTORER, 0x3c2d6302d0},
{0x40d0d4, [], SA_RESTORER, 0x3c2d6302d0}, 8) = 0
rt_sigaction(SIGTTOU, {SIG_DFL, [], SA_RESTORER, 0x3c2d6302d0},
{0x40d0d4, [], SA_RESTORER, 0x3c2d6302d0}, 8) = 0
rt_sigaction(SIGTTIN, {SIG_DFL, [], SA_RESTORER, 0x3c2d6302d0},
{0x40d0d4, [], SA_RESTORER, 0x3c2d6302d0}, 8) = 0
rt_sigaction(SIGWINCH, {SIG_DFL, [], SA_RESTORER, 0x3c2d6302d0},
{0x40d1ae, [], SA_RESTORER|SA_RESTART, 0x3c2d6302d0}, 8) = 0
open("3dor.prmtop", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
--- SIGSEGV (Segmentation fault) . 0 (0) ---
+++ killed by SIGSEGV (core dumped) +++

Complete strace of the process is in /tmp/123 on mesalane.


On 2/18/2011 3:20 PM, Lane Votapka via RT wrote:
> Hi Hans,
> I tried doing the some of my steps from my script line by line, and it
> fails if I do the "addions" command at some point followed by the
> "saveamberparm" command (very similar to what bugfix 2 is supposed to fix)
> If i run it in script form, it gives me the segmentation fault. If I run
> line by line like you did, then it gives me the same error that it gave
> and dumps the core. I searched that error online and found only a couple
> things where they mention the same problem (or similar ones) and they all
> just say that its fixed under a bugfix.
> Is it possible that I gave you the wrong page of bugfixes? The page says
> was last updated April 2010, but I've seen reports of the bug since then
> some forums. Should I try to contact the Amber staff directly?
> -Lane
> On Fri, Feb 18, 2011 at 2:44 PM, Hans Wunsch via RT<helpdesk.ics.uci.edu
>> Hi Lane,
>> I didn't get a segfault, but I did get a failure from saveamberparm:
>> [gtkleap]$ #would usually need to insert feature here to find out how
>> many ions were added, and use this in the calculation to add more
>> [gtkleap]$ saveamberparm dor 3dor.prmtop 3dor.inpcrd
>> sleap: exclude.cpp:54: void mort::prmtop::sort_key(std::vector<int,
>> std::allocator<int> >&, std::vector<int, std::allocator<int> >&):
>> Assertion `key.size() == value.size()' failed.
>> Aborted (core dumped)
>> I ran it as you with the following command:
>> sleap -f /lv_tmp/scratch/lvotapka/projects/cpaf/prepare/sleap3dor.in
>> Is that how you run it? Does that output look different from what you
>> are seeing?
>> Thanks,
>> Hans.
>> --
>> Hans Wunsch
>> Assistant Director of Computing Support
>> BSICS Computing Support Group
>> (949) 824-4035
>> helpdesk.ics.uci.edu

Hans Wunsch
Assistant Director of Computing Support
Bren:ICS Computing Support
(949) 824-4035
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Received on Tue Feb 22 2011 - 10:00:04 PST
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