Re: [AMBER] The err of sander.PUPIL

From: Aurum Bai <>
Date: Mon, 7 Jun 2010 17:04:18 +0800 (CST)

Thanks very much

When I use  "./configure_amber ifort" and then "make sander.PUPIL" , there are some err happen again:
ack -lmkl -lguide -lpthread \
    -lrt -lm -lc -L/home/bai/workdir/pupil-v1_3_0/lib -lPUPIL -lPUPILBlind
/home/bai/workdir/pupil-v1_3_0/lib/ undefined reference to `putdata_'
/home/bai/workdir/pupil-v1_3_0/lib/ undefined reference to `putresiduetype_'
/home/bai/workdir/pupil-v1_3_0/lib/ undefined reference to `putatomtype_'
/home/bai/workdir/pupil-v1_3_0/lib/ undefined reference to `putcoordinates_'

What is wrong with it? Could you give me some suggest?

--- On Mon, 6/7/10, Jason Swails <> wrote:

From: Jason Swails <>
Subject: Re: [AMBER] The err of sander.PUPIL
To: "AMBER Mailing List" <>
Date: Monday, June 7, 2010, 2:19 PM


sander.PUPIL I believe only works with a serial compilation (incompatible
with MPI for amber10).  At least this has been hard-coded into the
makefile.  You can get around this by going back to $AMBERHOME/src/ and
re-running configure_amber to run in serial.  Supposing you have ifort,

cd $AMBERHOME/src/
./configure_amber ifort

Then try and make sander.PUPIL.  If you have gfortran, replace ifort with
gfortran, etc.

Good luck!

P.S.  Also don't forget to make clean before you try to build sander.PUPIL

On Mon, Jun 7, 2010 at 1:13 AM, Aurum Bai <> wrote:

> Hello, everyone
> I follow the installation of PUPIL successfully. But when I compile the
> source of sander.PUPIL, I get the err information as below:
> "mv libdivcon.a ../src/qmmm/
> make[2]: Leaving directory `/home/bai/workdir/amber10/src/dcqtp/mod'
> make[1]: Leaving directory `/home/bai/workdir/amber10/src/dcqtp'
> ./checkserconf
> Error: ../config_amber.h is not set up for serial compilation
> make: *** [checkserconf] Error 1
> "
> what is wrong with it? How do I solve it?
> Thanks
> javacfish
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
AMBER mailing list
Received on Mon Jun 07 2010 - 02:30:06 PDT
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