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
Received on Wed Jun 08 2016 - 13:30:02 PDT
