Re: [AMBER-Developers] AT 1.3 config fails for alternate gnu location

From: Lachele Foley <>
Date: Wed, 25 Nov 2009 15:15:24 -0500

>> ./configure: line 744: ./testp: No such file or directory
>> Unable to compile a Fortran program using gfortran -O0

> This indicates that the /usr/local/bin fortran installation is completely hosed....

Oh... Worked fine the last time I installed Amber, but there have been updates since then. Might be the machine needs a reboot, too. I'll try that then reinstall if I have to.

For Jason: I had tried the higher path in the tree, but it didn't work. That's why I tried pointing to the exact directory. Apparently, Dave is right.

The only other possibility is that the code wants a 32-bit version and I'm pointing it to a 64-bit version. 64-bit machines are common now, though, so that seems unlikely.

Regarding setting paths and such, Ben saw my point that resetting paths can cause confusion. Too often, I accidentally type something like PATH=$newbit:$PATh and suddenly everything dies. This is why I like the idea of being able to specify separately. But, like Dave said, it will only cause confusion to people who are used to such things. I'll double-check the config.h not happening. I recall that, because I think I thought "oh... I'll just add the location to the path," but not being able to. But, I was tired, etc.

Thanks for the How-To. Making tea doesn't take enough time, though. I suggest renting a movie.

I don't have enough knowledge to comment on Vlodomyr's suggestions, though they sound interesting.

:-) Lachele
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
----- Original Message -----
From: case
To: AMBER Developers Mailing List
Sent: Tue, 24 Nov 2009 22:19:42
Subject: Re: [AMBER-Developers] AT 1.3 config fails for alternate gnu
> On Tue, Nov 24, 2009, Lachele Foley wrote:
> > I have an alternate gcc/gfortran installed on a system in /usr/local/bin
> > (etc.).  If I rearrange my PATH so that the system sees the original
> > install (in /usr/bin), AT configures and compiles (testing now).  If I
> > leave my path so it finds the gcc/gfortran in /usr/local/bin first, the
> > configure fails with complaints about gfortran and netcdf.
> > 
> > If there's a way in the configure script to specify alternate library
> > paths, I don't see it.  I can alter the config.h file, of course, but
> > not if the configure script never makes one.
> Well, this is a bit of a problem.  If the netcdf configuration fails, it
> should still make a legal config.h, just with netcdf usage turned off.  This
> sounds like a bug in the configure script.
> The second problem is more problematical: should we allow users to point
> to their preferred compilers by some means other than adjusting their PATH
> variable?  I'm inclined to think not: users that know enough to have
> multiple
> compilers installed in their systems can surely temporarily adjust their
> variable when configuring and compiling Amber, returning it to its original
> state later if desired.
> We certainly could (as Volodymyr will not doubt suggest) pick up environment
> variables so that Lachele could enter something like this:
>    env CC=/usr/bin/gcc FC=/usr/bin/gfortran CFLAGS="-O2" (etc) \
>       ./configure -static -3drism  (etc)
> My (mildish) objection is that we have to make sure this all works OK, we
> have to document it, and (the real problem): we have to try to remotely
> debug all kinds of weird behavior people will report because they actually
> have a "CC" environment variable without knowing it.
> My general feeling is that it is better to make an experienced user like
> Lachele temporarily edit her PATH, than to make things harder than they
> already are for novice users.
> > 
> > Testing the gfortran compiler:
> >      gfortran -O0 -o testp testp.f
> > /usr/bin/ld: cannot find -lgfortranbegin
> > collect2: ld returned 1 exit status
> > ./configure: line 744: ./testp: No such file or directory
> > Unable to compile a Fortran program using gfortran -O0
> This indicates that the /usr/local/bin fortran installation is completely
> hosed....
> > 
> > checking if Fortran "byte" is C "signed char"... configure: error: Could
> not link conftestf.o 
> of course the fortran part of netcdf won't work either.  Basically we
> have gone over to requiring a working fortran 90 compiler for AmberTools.
> ....dac
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Received on Wed Nov 25 2009 - 12:30:02 PST
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