I'm getting disturbing output after doing "./update_amber --upgrade" and
then recompiling. I am running RHEL Linux 7.3.
After I do
./update_amber --upgrade
It completes with no errors. Then I do:
./configure gnu
It completes with no errors. Then I do
source amber.sh
No errors. Then I do:
make install
and the last section of output gives me this:
make[2]: Leaving directory `/home/amber16/AmberTools/src/saxs'
(cd mm_pbsa && make install)
make[2]: Entering directory `/home/amber16/AmberTools/src/mm_pbsa'
gfortran -fPIC -I/home/amber16/include -I/home/amber16/include -c -o
make_crd_hg.o make_crd_hg.F
gfortran -DBINTRAJ -DEMIL -fPIC -I/home/amber16/include
-I/home/amber16/include -o /home/amber16/bin/make_crd_hg make_crd_hg.o \
../lib/amopen.o ../lib/mexit.o
cp mm_pbsa.pl mm_pbsa_statistics.pl /home/amber16/bin
cp *.pm /home/amber16/lib/perl/mm_pbsa/
make[2]: Leaving directory `/home/amber16/AmberTools/src/mm_pbsa'
(cd FEW && make install)
make[2]: Entering directory `/home/amber16/AmberTools/src/FEW'
gcc miscellaneous/draw_membrane2.c -lm -o miscellaneous/draw_membrane2
AMBER_PREFIX=/home/amber16 AMBER_SOURCE=/home/amber16 /bin/sh setup.sh
Checking if your kit is complete...
Looks good
Only one of PREFIX or INSTALL_BASE can be given. Not both.
make[3]: Entering directory
`/home/amber16/AmberTools/src/FEW/additional_libs/PerlMol-0.3500'
make[3]: *** No targets specified and no makefile found. Stop.
make[3]: Leaving directory
`/home/amber16/AmberTools/src/FEW/additional_libs/PerlMol-0.3500'
make[3]: Entering directory
`/home/amber16/AmberTools/src/FEW/additional_libs/PerlMol-0.3500'
make[3]: *** No rule to make target `install'. Stop.
make[3]: Leaving directory
`/home/amber16/AmberTools/src/FEW/additional_libs/PerlMol-0.3500'
cp -f /home/amber16/AmberTools/src/FEW/FEW.pl /home/amber16/bin
cp: '/home/amber16/AmberTools/src/FEW/FEW.pl' and '/home/amber16/bin/FEW.pl'
are the same file
make[2]: *** [install] Error 1
make[2]: Leaving directory `/home/amber16/AmberTools/src/FEW'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/home/amber16/AmberTools/src'
make: *** [install] Error 2
[root.t7910 amber16]#
Then I do:
make test
and get this:
Finished serial test suite for Amber 17 at Wed Apr 19 00:37:05 EDT 2017.
make[2]: Leaving directory `/home/amber16/test'
162 file comparisons passed
0 file comparisons failed
0 tests experienced errors
Test log file saved as
/home/amber16/logs/test_amber_serial/2017-04-19_00-28-56.log
No test diffs to save!
make[1]: Leaving directory `/home/amber16/test'
Summary of AmberTools serial tests:
1930 file comparisons passed
34 file comparisons failed
4 tests experienced errors
Test log file saved as
/home/amber16/logs/test_at_serial/2017-04-18_22-24-42.log
Test diffs file saved as
/home/amber16/logs/test_at_serial/2017-04-18_22-24-42.diff
[root.t7910 amber16]#
Is this the expected behavior?
Jim
-----Original Message-----
From: David Case [mailto:david.case.rutgers.edu]
Sent: Monday, April 17, 2017 9:28 PM
To: amber.ambermd.org
Subject: [AMBER] Release of AmberTools17
On behalf of many developers (see
http://ambermd.org/contributors.html), I
am pleased to announce the release of AmberTools17. This contains all of
the Amber programs except pmemd, and is intended to work alongside (in the
same directory tree) as pmemd from Amber16.
For information about new features, downloading and installation, please
visit:
http://ambermd.org/#AmberTools
If you already have AmberTools16, just type "./update_amber --upgrade"
in your AMBERHOME directory, and follow the prompts. If you are a new user,
please visit the web page above. We are also providing, for the first time,
a binary (pre-compiled) version for Linux and MacOS using the conda package
manager; again see the web page above for details.
Thanks to everyone who helped make this possible.
....dac
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 19 2017 - 11:30:02 PDT
