AMBER Archive (2008)

Subject: Re: RE: AMBER: the install problem

From: hklwatergod (
Date: Mon Jul 28 2008 - 09:22:58 CDT

Hi Ross
i adopt your suggestion and first i put the amber10 and amber10tools in the same directory,and then i install the ambertools and make test. all passed. second, i install the amber10 using ifort. when i type ./configure_amber -static ifort_ia32,the following errors:
Setting AMBERHOME to /usr/local/amber10
Setting up Amber configuration file for architecture: ifort_ia32
Using parallel communications library: none
The MKL_HOME environment variable is not defined.
    The MKL is recommended for optimal performance.

Testing the C compiler:
      gcc -m32 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -o testp testp.c

Testing the Fortran compiler:
     ifort -w95 -vec_report0 -mp1 -O0 -o testp testp.f

  ------ Configuring the netCDF libraries: --------

Configuring netcdf; (may be time-consuming)
./configure: line 1: type: -m32: not found
NETCDF configure succeeded.
The configuration file, config_amber.h, was successfully created.
i ignore the ./configure: line 1: type: -m32: not found error and the install the amber. The amber10 is installed.
when i make test, there is another error following:

cd LES && ./Run.PME_LES
  Amber 8 ADDLES and SANDER.LES test:
Segmentation fault
  ./Run.PME_LES: Program error
make: *** [test.sander.LES] Error 1

what is wrong ??
thanks a lot~!


发件人: Ross Walker
发送时间: 2008-07-27 16:05:03
主题: RE: AMBER: the install problem

>Configuring netcdf; (may be time-consuming)
>./configure_amber: line 1211: cd: netcdf/src: No such file or directory
>netcdf configure returned 1
>NETCDF configure failed! Check the netcdf_config.log file

>what is wrong???

Did you download and install amber tools before trying to build amber? You
need to do this first since the netcdf libraries etc required by amber and
built as part of the amberstool installation.

I would also be helpful to look in the netcdf_config.log file and see what
that says. Posting that with your message can help as well.


|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
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