Just looked at your test case and I know what's wrong. Remove '-r
/dev/null' from your command line. The default restart format in
Amber16 changed to NetCDF, and NetCDF routines get cranky if you try
to open /dev/null.
-Dan
On Fri, Dec 1, 2017 at 2:52 AM, Paul Mortenson <Paul.Mortenson.astx.com> wrote:
> Hi Dan,
>
> Thanks for your suggestion, unfortunately that has not worked either. [Added ". $AMBERHOME/amber.sh" before each sander command. 14 works fine, 16 fails with the same error.]
>
> What makes you think the error is OS-related - as AMBER14 works fine I had assumed this was an AMBER16 issue? Does my test case run OK in your environment? We're running CentOS 7, and I don't think we've done anything particularly unusual with the setup. Out of interest, what does the error message actually mean?
>
> Thanks,
> Paul
>
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: 30 November 2017 18:58
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] imin=5 not working in AMBER16?
>
> Hi,
>
> Sander will automatically determine the input trajectory format for postprocessing. Since the error is OS-related, probably something is going on with your system. I notice in the test script in your attachment you're setting AMBERHOME but not sourcing amber.sh. Perhaps there's some library incompatibility occurring? Try sourcing the amber.sh script in your Amber 16 directory before running.
>
> -Dan
>
> On Wed, Nov 29, 2017 at 10:19 AM, Paul Mortenson <Paul.Mortenson.astx.com> wrote:
>> Hi,
>>
>> I'm having trouble getting sander to work with imin=5 (post-processing trajectory files). I have attached a simple test case which works fine for AMBER14, but not with AMBER16.
>>
>> Sander crashes before outputting any energies, with the following error message:
>>
>> sander: posixio.c:232: px_pgout: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed.
>>
>> Program received signal SIGABRT: Process abort signal.
>>
>> Backtrace for this error:
>> #0 0x7F29152256F7
>> #1 0x7F2915225D3E
>> #2 0x7F291472A26F
>> #3 0x7F291472A1F7
>> #4 0x7F291472B8E7
>> #5 0x7F2914723265
>> #6 0x7F2914723311
>> #7 0xA1E92C in px_pgout at posixio.c:?
>> #8 0xA1F4F6 in px_get at posixio.c:?
>> #9 0xA1F6FD in ncio_px_get at posixio.c:?
>> #10 0xA18137 in ncio_get
>> #11 0xA21D67 in putNCvx_char_char at putget.c:?
>> #12 0xA29DE5 in writeNCv at putget.c:?
>> #13 0xA2ABA4 in NC3_put_vara
>> #14 0xA12A26 in NC_put_vara at dvarput.c:?
>> #15 0xA12F61 in NCDEFAULT_put_vars
>> #16 0xA13A56 in NC_put_vars at dvarput.c:?
>> #17 0xA14902 in nc_put_vars_text
>> #18 0xA0B414 in nf_put_vars_text_
>> #19 0xA01829 in __netcdf_MOD_nf90_put_var_1d_text
>> #20 0x68DB6B in __ambernetcdf_mod_MOD_nc_create
>> #21 0x691F41 in __binrestart_MOD_write_nc_restart
>> #22 0x544B4B in master.0.minrit_.part.0.constprop.1 at minrit.F90:?
>> #23 0x4EEB9A in runmin_
>> #24 0x4DA2F4 in __trajenemod_MOD_trajene
>> #25 0x4D83E3 in sander_
>> #26 0x4CE738 in MAIN__ at multisander.F90:?
>>
>> Does anyone have any suggestions?
>>
>> Thanks,
>> Paul Mortenson
>>
>> This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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>
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>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Dec 01 2017 - 06:00:11 PST
