[AMBER-Developers] misc configure issues

From: Scott Brozell <sbrozell.rci.rutgers.edu>
Date: Thu, 20 Mar 2014 13:03:40 -0400

Hi,

Based on failed builds on various Rutgers and OSC machines in the git master
configure needs work:

1.
fftw-3.3 related:
a. fftw-3.3 configure succeeds, build succeeds, hundreds of tests involving
   several executables fail. This happened on machines at Rutgers and OSC
   using gnu and intel compilers.
b. The messages and logic in configure related to -nofftw3 are incomplete or
   inconsistent; mdgx does not appear to completely covered; sander appears
   to be completely uncovered.
c. There is no easy way to override Amber's fftw with a pre-existing and
   working fftw-3.3.
d. When i load an fftw-3.3 module, as a potential easy way to get the library
   and bypass the above,
   i then get libnetcdf.so.7 cannot open shared objects errors; this one may
   be me...see 3.

2.
If zlib or libbz2 is missing then configure does not fail, it merely spews
Not found in a messy format, but the build does fail.

3.
It still seems too easy for users to get into trouble, like above,
and then get into a state where merely re-configuring and re-building
does not effectively do a distclean, ie, lead to a completely fresh start.
Again this one might be me ...

scott

---
---
Configuring fftw-3.3 (may be time-consuming)...
    fftw-3.3 configure succeeded.
.
.
.
ifort -DBINTRAJ -DEMIL    -FR -I../pbsa -I../sqm -I../rism -I../../../include  -I/net/casegroup2p/u2/sb
rozell/amber/ambercasegroup/include -I/net/casegroup2p/u2/sbrozell/amber/ambercasegroup/include    -o /
net/casegroup2p/u2/sbrozell/amber/ambercasegroup/bin/sander
...
         -lrism -lfftw3 -larpack -llapack -lblas    -lsvml \
         -shared-intel      
ifort -DBINTRAJ -DEMIL    -c -O0 -FR -I../pbsa -I../sqm -I../rism -I../../../include  -I/net/casegroup2p/u2/sbrozell/amber/ambercasegroup/include -I/net/casegroup2p/u2/sbrozell/amber/ambercasegroup/include    -DRISMSANDER -o nose_hoover_init_LES.o nose_hoover_init_LES.F90
.
.
.
Running test to make dna duplex:
./duplex: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
./Run.duplex: Program error
.
.
.
cd dmp && ./Run.dmp
../../bin/sander: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
  ./Run.dmp:  Program error
---
---
Checking for zlib: testp.c:2:18: fatal error: zlib.h: No such file or directory
 #include "zlib.h"
                  ^
compilation terminated.
./configure2: line 2005: ./testp: No such file or directory
Not found.
Checking for libbz2: testp.c:2:19: fatal error: bzlib.h: No such file or directory
 #include "bzlib.h"
                   ^
compilation terminated.
./configure2: line 2029: ./testp: No such file or directory
Not found.
.
.
.
(cd cphstats && make install)
make[2]: Entering directory `/net/casegroup2/u2/sbrozell/amber/amber/AmberTools/src/cphstats'
g++   -O3  -c main.cpp
In file included from main.cpp:10:0:
cpout.h:11:18: fatal error: zlib.h: No such file or directory
 #include "zlib.h"
                  ^
compilation terminated.
---
---
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Received on Thu Mar 20 2014 - 10:30:02 PDT