AMBER Archive (2008)

Subject: Re: AMBER: Some Problems With the Installation of Ambertools

From: Manikandan Chandrasekaran (mxchandrasek_at_ualr.edu)
Date: Fri Sep 19 2008 - 14:49:41 CDT

Hi David,

These are the steps which I tried to fix the bugs.

Have G95 compiler for Solaris from GNU(g95.org). Configure_at gcc looked for g77 and gfortran.
As it didn't find, it wasn't able to run the test program and said will be unable to run mopac.So, created a soft link with the name gfortran for g95.
ln -s /usr/sfw/bin/g95 /usr/bin/gfortran (Thanks Francis!)
And still there were errors resulting because of the -fno-automatic in fflags of the Config_At file. So tried removing the -fno-automatic and then tried configuring it.The program configured successfully.

make -f Makefile_at install(previously without any changes)

nmode.c: In function `lnorm':
nmode.c:1172: error: `_Imaginary_I' undeclared (first use in this function)
nmode.c:1172: error: (Each undeclared identifier is reported only once
nmode.c:1172: error: for each function it appears in.)
*** Error code 1
make: Fatal error: Command failed for target `nmode.o'
Current working directory /usr/local/amber10/amber10/src/nab
*** Error code 1
make: Fatal error: Command failed for target `install'

make -f Makefile_at clean(as suggested!)

make: Fatal error in reader: Makefile, line 12: Unexpected end of line seen
Current working directory /usr/local/amber10/amber10/src/gleap/mortsrc/common
*** Error code 1
make: Fatal error: Command failed for target `clean'
Current working directory /usr/local/amber10/amber10/src/gleap/mortsrc
*** Error code 1
make: Fatal error: Command failed for target `clean'
Current working directory /usr/local/amber10/amber10/src/gleap
*** Error code 1
make: Fatal error: Command failed for target `clean'

config.h file - Arpack Library Scanning(correct location) and the change(underlined)

LIBDIR=/usr/local/amber10/amber10/lib
FLIBS= $(LIBDIR)/libsym.a $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a
 $(LIBDIR)/f2c.a

CFLAGS= -m32 -DBINTRAJ -DUSE_AMBER_C9XCOMPLEX $(AMBERBUILDFLAGS)

make -f Makefile_at install (after the changes)

gcc: /usr/local/amber10/amber10/lib/arpack.a: No such file or directory
cc failed!
*** Error code 1
make: Fatal error: Command failed for target `matextract'
Current working directory /usr/local/amber10/amber10/src/nss
*** Error code 1
make: Fatal error: Command failed for target `install'

find . -name "arpack.a" -print( there s only one arpack inside carpack..Are both the arpacks same?)

./usr/local/amber10/amber10/src/carpack/arpack.a

Can I copy this one out to the lib folder? I am not sure! Can you please tell, the steps which I followed are in the right direction? Also a suggestion is needed on how to move further.

Thanks
Mani

----- Original Message -----
From: "David A. Case" <case_at_biomaps.rutgers.edu>
Date: Thursday, September 18, 2008 1:41 pm
Subject: Re: AMBER: Some Problems With the Installation of Ambertools
To: amber_at_scripps.edu

> On Thu, Sep 18, 2008, Manikandan Chandrasekaran wrote:
>
> > gcc: /usr/local/amber10/amber10/lib/arpack.a: No such file or
> > directory
>
> This is quite odd.  There is no configure option that ever skips
> compiling
> the arpack library.  You should try the following:
>
> cd $AMBERHOME/src
> make -f Makefile_at clean
> make -f Makefile_at install
>
> Look carefully for any errors related to arpack
> compilation.  It is the
> third thing that is compiled.
>
> Is your tree really under /usr/local/amber10/amber10  (two
> "amber10"'s?)Could there be some problem with your AMBERHOME
> environment variable?
>
> ...dac
> -----------------------------------------------------------------
> ------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>       to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu