RE: AMBER: Amber Installation Error

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 15 Jun 2007 12:25:28 -0700

Dear Joe,
 
It looks to me like you didn't start from a clean installation. You can try
doing "make clean" inside $AMBERHOME/src/ and then "make" and see if this
works. It should do. Alternatively I would go back to the original tar file
from the cd and uncompress this into a clean directory so that you know
where you are starting from.
 
Try the make clean first.
 
All the best
Ross
 
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Joe Nolan
Sent: Friday, June 15, 2007 08:58
To: amber.scripps.edu
Subject: AMBER: Amber Installation Error


Hello again Amber users,
I seem to be running into a problem with Amber9 while trying to install on
an AMD Opteron dual-core system running RHEL 5, with the gfortran compiler.
I did a plain configure with "./configure gfortran" and the resulting errors
are listed:

ake[2]: Entering directory `/usr/local/amber9/src/lib'
make[2]: `amopen.o' is up to date.
make[2]: Leaving directory `/usr/local/amber9/src/lib'
make[2]: Entering directory `/usr/local/amber9/src/lib'
make[2]: `mexit.o' is up to date.
make[2]: Leaving directory `/usr/local/amber9/src/lib'
make[2]: Entering directory `/usr/local/amber9/src/lib'
make[2]: `nxtsec.o' is up to date.
make[2]: Leaving directory `/usr/local/amber9/src/lib'
gfortran -o ambpdb ambpdb.o forFIRSTtype.o forFIRSTbond.o forFIRSThbond.o
forFIRSTteth.o forFIRSToutp.o ../lib/amopen.o ../lib/mexit.o
../lib/nxtsec.o
gfortran -o nucgen nucgen.o ngfil.o ../lib/amopen.o ../lib/mexit.o
../lib/nxtsec.o
g++ -c -o elsize.o elsize.cc
elsize.cc:74:21: error: fstream: No such file or directory
elsize.cc:75:21: error: string: No such file or directory
elsize.cc:80:20: error: iostream: No such file or directory
elsize.cc: In function ‘int main(int, char**)’:
elsize.cc:117: error: ‘exit’ was not declared in this scope
elsize.cc:124: error: ‘strcmp’ was not declared in this scope
elsize.cc:145: error: ‘strcmp’ was not declared in this scope
elsize.cc:160: error: ‘calloc’ was not declared in this scope
elsize.cc:171: error: ‘exit’ was not declared in this scope
elsize.cc:233: error: ‘exit’ was not declared in this scope
elsize.cc:295: error: ‘exit’ was not declared in this scope
elsize.cc:339: error: ‘exit’ was not declared in this scope
elsize.cc: In function ‘atom_count GetNumberOfAtoms(const char*, int)’:
elsize.cc:498: error: ‘ifstream’ was not declared in this scope
elsize.cc:498: error: expected `;' before ‘scanstream’
elsize.cc:499: error: ‘scanstream’ was not declared in this scope
elsize.cc:504: error: ‘exit’ was not declared in this scope
elsize.cc:511: error: ‘string’ was not declared in this scope
elsize.cc:511: error: expected `;' before ‘junk’
elsize.cc:514: error: ‘junk’ was not declared in this scope
elsize.cc: In function ‘atom_count ReadAtomicCoordinates(const char*, int,
atom_count, double*, double*, double*, double*, double*)’:
elsize.cc:559: error: ‘ifstream’ was not declared in this scope
elsize.cc:559: error: expected `;' before ‘datastream’
elsize.cc:560: error: ‘datastream’ was not declared in this scope
elsize.cc:565: error: ‘exit’ was not declared in this scope
elsize.cc:570: error: ‘string’ was not declared in this scope
elsize.cc:570: error: expected `;' before ‘junk’
elsize.cc:590: error: ‘junk’ was not declared in this scope
make[1]: *** [elsize.o] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/etc'
make: *** [serial] Error 2

I'm no programming expert, but my guess is user error on my end of some
sort. Any and all ideas are welcome and truly appreciated!
- Joe Nolan




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Received on Sun Jun 17 2007 - 06:07:36 PDT
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