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Old 01-22-2009, 03:33 PM   #1
beartofear
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Compiling and Installation Help with Qnifft (Calculation/Biochemistry Program)


Hello everyone.

I want to say I'm a totally new to Linux and in fact I only decided to try out Linux as I'm in biochemistry and a program I want to use it necessitates me having linux (although the benefits of Kubuntu seem very numerous after I installed it and hopefully the necessary compilers).

Anyway, my attempts to install and compile the program are failures to this point. According to the README section, I need to alter the Makefiles to reflect my compiler, and there is a Makefile present Makefile_gnu which is for linux which uses the g77 compiler (which should be installed now).

When I run the Install.com I get the following errors (bolded):

********

Installing QNIFFT

delphi root directory set to /home/gijoe/Downloads/qnifft
environment variable DELDIR defined


path now set to /usr/local/sbin /usr/local/bin /usr/sbin /usr/bin /sbin /bin /us r/games

platform: SGI (1) GNU (2) Compaq (3) Lahey Compiler (4) Other (5)?
2

make -n -f $DELDIR/source/Makefile_gnu -f Makefile

compiling utility programs

make: $DELDIR/source/Makefile_gnu: No such file or directory
make: *** No rule to make target `$DELDIR/source/Makefile_gnu'. Stop.
make: $DELDIR/source/Makefile_gnu: No such file or directory
make: *** No rule to make target `$DELDIR/source/Makefile_gnu'. Stop.
make: $DELDIR/source/Makefile_gnu: No such file or directory
make: *** No rule to make target `$DELDIR/source/Makefile_gnu'. Stop.
make: $DELDIR/source/Makefile_gnu: No such file or directory
make: *** No rule to make target `$DELDIR/source/Makefile_gnu'. Stop.

compiling main program

make: $DELDIR/source/Makefile_gnu: No such file or directory
make: *** No rule to make target `$DELDIR/source/Makefile_gnu'. Stop.
make: $DELDIR/source/Makefile_gnu: No such file or directory
make: *** No rule to make target `$DELDIR/source/Makefile_gnu'. Stop.
make: $DELDIR/source/Makefile_gnu: No such file or directory
make: *** No rule to make target `$DELDIR/source/Makefile_gnu'. Stop.
make: $DELDIR/source/Makefile_gnu: No such file or directory
make: *** No rule to make target `$DELDIR/source/Makefile_gnu'. Stop.

List of compiled programs:
total 0


To run the programs in future place these 2 commands in your log file:
setenv DELDIR /home/gijoe/Downloads/qnifft
set path=( $path /home/gijoe/Downloads/qnifft/bin )


Finished Installing QNIFFT - run the examples, and go

****

I guess I'm not sure why it says it cannot find the file if in fact I can see a Makefile_gnu in the directory listed.

Thanks for any help you might have.
 
Old 01-22-2009, 10:34 PM   #2
weibullguy
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Open Install.com in your favorite editor. Find this line (should be line 28) and change the single quotes to double quotes.
Code:
set compile = 'make -n -f ${DELDIR}/source/Makefile_gnu -f Makefile'
Also, the -n option to make means "dry run". If you want to actually build the application, you'll need to remove the -n also. So the line should look like
Code:
set compile = "make -f ${DELDIR}/source/Makefile_gnu -f Makefile"
It should build after these changes.

Also, g77 has been replaced by gfortran in newer versions (4.1.X and 4.2.X) of gcc. I didn't try to build it with gfortran so it might work.
 
Old 01-23-2009, 03:11 AM   #3
knudfl
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Welcome to Linux Questions.

It works fine with " g77 -> /usr/bin/g77-3.3.6* "

And of course the edited Makefile from weibullguy.

....

Last edited by knudfl; 01-23-2009 at 03:42 AM.
 
Old 01-23-2009, 11:20 AM   #4
beartofear
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Hey guys,

Thanks for the help it is most appreciated.

So I tried the modified makefile, and I tried with compiler g77 and g77-3.4 (which I have via the package manager on Kubuntu) and it did seem to compile the programs.

However, in the course of compiling, it seemed that it was ignoring MANY variables, and it seemed to be happening along the way, and here is the sample of what was popping up along the way.

*******************************************************************

Makefile:8: warning: overriding commands for target `.f.o'
/home/gijoe/Downloads/qnifft/source/Makefile_gnu:12: warning: ignoring old commands for target `.f.o'
/bin/cp qdiffpar129.h qdiffpar.h
echo " data lstmod / ' `date`'/" > lstmod.h
g77-3.4 -fno-ugly -O2 -Wall -ffixed-line-length-132 -c dtstmp.f
dtstmp.f: In subroutine `dtstmp':
dtstmp.f:29: warning:
call date(day)
^
Intrinsic `DATE', invoked at (^), known to be non-Y2K-compliant [info -f g77 M Y2KBAD]
In file included from dtstmp.f:29:
dtstmp.f:21: warning: unused variable 'hour'
g77-3.4 -fno-ugly -O2 -Wall -ffixed-line-length-132 qnifft22.f elb.f up.f charge.f radius.f getpdb.f phintp.f scaler.f chrgit.f setbc.f wrteps.f cputime.f phierg.f inewt.f getpar.f qhelp.f chrgal.f dtstmp.f dmpeps.f phirxn.f phifrc.f sasgen.f mapgen.f girdgen.f utility.f pntchk.f mkepsd.f
qnifft22.f: In program `qnifft22':
In file included from qnifft22.f:12:
qdiffpar.h:81: warning: unused variable 'atm'
qdiffpar.h:80: warning: unused variable 'snum'
qdiffpar.h:80: warning: unused variable 'rnum'
qdiffpar.h:79: warning: unused variable 'res'
qdiffpar.h:79: warning: unused variable 'sres'
qdiffpar.h:78: warning: unused variable 'schn'
qdiffpar.h:78: warning: unused variable 'chn'
charge.f: In subroutine `getcfil':

*************************************************************************

This repeated in various sections, ignoraing many of the same variables. It seems that it did finish compiling, but when I ran the programs the calculations came back from very different answers than I had received previously using the program on another computer. I'm wondering if the compilers are ignoring critical variables?

Again thanks for the help so far as at least now its doing something!
 
Old 01-23-2009, 03:54 PM   #5
beartofear
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Well, as an update.

Apparently the errors were a red herring.

Program is now compiled and functioning.
 
Old 01-23-2009, 04:30 PM   #6
weibullguy
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They're not errors, they're warnings. If they had been errors, the make would have exited. The warning you posted are telling you that the variables were defined, but never used. No biggie, unless they were meant to be used.
 
  


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