This is my program, and while we haven't seen this problem before, it's
obviously up to me to figure this one out. Let's take this offline and
I'll see if I can solve the problem.
Dave
On Wed, Jun 8, 2016 at 4:28 PM, Kenneth Hoste <kenneth.hoste.ugent.be>
wrote:
> Hello,
>
> I'm trying to figure out a weird problem when installing Amber 14 +
> AmberTools 15, I hope it looks familiar to someone here who could
> provide pointers on the possible cause.
>
> Basically, I'm seeing "make test" hang as follows:
>
> make test
> \_ /bin/sh ./test_at_serial.sh
> \_ make -k -f Makefile test.serial
> | \_ /bin/sh -c cd mdgx/1p7e && ./Test.1p7e
> | \_ /bin/bash ./Test.1p7e
> | \_ /<prefix>/software/Amber/14-intel-2016a/bin/mdgx -O
> -i mdgx.in
>
> The mdgx is logging is taking 100% CPU (single-core), and is logging
> profusely to <prefix>/test/mdgx/1p7e/gb30.out, albeit mostly with
> newlines...
>
> The head of the log file is pasted below, all other lines are empty
> lines (*lots* of them); this is the size of the log file after 45m:
>
> $ wc -l
> <prefix>/software/Amber/14-intel-2016a/AmberTools/test/mdgx/1p7e/gb30.out
> 16869489392
>
> The '/user/scra' bit at the end of the log file is copy-pasted as it is
> included in the log file, and is the start of the installation path of
> Amber.
> It seems to be cut off for some reason, after which the test goes into
> lala-land and starts printing newlines.
>
> The problem seems to be the length of the path: if I install Amber to a
> shorter path, the test does not hang.
>
> However, the path is not extremely long according to me; the full path
> to the test/mdgx/1p7e/gb30.out log file is just 151 characters long (all
> ASCII characters).
>
> Does this look familiar to someone? Is there a way to fix it (other than
> using a shorter install path, obviously)?
>
>
> Contents of test/mdgx/1p7e/gb30.out:
>
>
> <++>-----------------------------------------------------------------------<++>
> <++> mdgx: A molecular dynamics engine in the AMBER suite of
> programs <++>
> <++> <++>
> <++> Written by David S. Cerutti, Case Group
> (2009) <++>
>
> <++>-----------------------------------------------------------------------<++>
>
> Run on Wed Jun 8 15:53:52 2016
>
> INPUT FILE ASSIGNMENTS:
> Designation Base name Suffix
> ----------------- ---------------------------------------------
> ----------
> Input File mdgx.in NONE
> Input Coordinates inpcrd NONE
> Topology prmtop NONE
>
> OUTPUT FILE ASSIGNMENTS:
> Designation Base name Suffix
> ----------------- ---------------------------------------------
> ----------
> State Information gb3 .out
> Restart file gb3 .rst
>
> !!! Output overwriting is ENABLED !!!
>
> <++>-----------------------------------------------------------------------<++>
>
> INPUT LINE TEXT:
>
> /user/scra
>
>
>
>
>
> regards,
>
> Kenneth
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 08 2016 - 15:00:02 PDT
