On Dec 17, 2012, at 6:39 AM, Sindrila Dutta banik <sindrila.duttabanik.yahoo.com> wrote:
> Dear all,
>
> I am trying to install amber in lab-cluster. First I untar, then set
> environment and bug fixes. Now I am trying to create the configuration
> file and compile everything. this gives the following error: [sindrila.master9 src]# ./configure -p4 gfortran
> AMBERHOME is set to /home/sindrila/amber9
> Setting up Amber configuration file for architecture: gfortran
> Using parallel communications library: none
> The MKL_HOME environment variable is not defined. The configuration file, config.h, was successfully created. [sindrila.master9 src]# make serial
> Starting installation of Amber9 (serial) at Mon Dec 17 16:42:14 IST 2012.
> cd lib; make install
> make[1]: Entering directory `/home/sindrila/amber9/src/lib'
> cpp -traditional -P -xassembler-with-cpp -Dsecond=ambsecond new2oldparm.f > _new2oldparm.f gfortran -c -O0 -fno-second-underscore -march=pentium4 -mfpmath=sse -msse
> -msse2 -malign-double -march=nocona -o new2oldparm.o _new2oldparm.f
> _new2oldparm.f:0: error: -malign-double makes no sense in the 64bit mode
> make[1]: *** [new2oldparm.o] Error 1
> make[1]: Leaving directory `/home/sindrila/amber9/src/lib'
> make: *** [serial] Error 2
To address this specific error, you need to get rid of the -malign-double flag in your config.h file.
Please note that this will almost certainly not be your only error. I would strongly suggest upgrading to Amber12, since amber 9 is now ~6-7 years old, and will probably not build easily on modern systems. The alternative is, of course, to get ready to spend a lot of time with google to look up and solve all of the individual build error messages that pop up.
Also, since 64-bit systems were much rarer back then, there are numerous issues with segfaults and errors that have since been fixed due to 64-bit incompatibilities in amber9.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Dec 17 2012 - 06:30:04 PST
