AMBER Archive (2006)

Subject: Re: AMBER: Amber 9 installation problem

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Oct 19 2006 - 12:55:54 CDT

Hi,
 
 the following line has worked for me.
 
  export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/opt/intel/fce/9.0/lib:\
 /opt/intel/mkl/8.1.1/lib/em64t"

 and Amber9 has passed all the tests (well except for a couple of failures due to very tiny energy differences from reference outputs. This I think may be expected when users prefer different compilers...
 One thing however I do not understand is the antechamber test for sustiva. partial atomic charges show high deviations from reference values as seen below
 possible FAILURE: check sustiva.mol2.dif
 /home/jenk/amber9/test/antechamber/sustiva
 7c7
 < 1 C1 0.728 1.403 0.255 ca 1 SUS 0.049
 ---
> 1 C1 0.728 1.403 0.255 ca 1 SUS 0.050
 10,11c10,11
 < 4 C3 0.290 0.932 0.158 c3 1 SUS 0.315
 < 5 C4 1.635 0.352 0.032 c1 1 SUS 0.196
 ---
> 4 C3 0.290 0.932 0.158 c3 1 SUS 0.314
> 5 C4 1.635 0.352 0.032 c1 1 SUS 0.197
 21,22c21,22
 < 15 C9 0.117 1.500 1.582 c3 1 SUS 0.619
 < 16 F1 1.056 2.097 1.693 f 1 SUS 0.229
 ---
> 15 C9 0.117 1.500 1.582 c3 1 SUS 0.620
> 16 F1 1.056 2.097 1.693 f 1 SUS 0.228
 
 I plan on looking into this later...
 
 regards,
 
 jenk.
 
 
 
 
 thanks for the tip.
 
 regards,
 
 jenk
 
Mark Williamson <Mark.Williamson_at_imperial.ac.uk> wrote: Cenk Andac wrote:
> Dear Amber community,
> I have installed Amber9 for the first time using ifortx86_64 and intel's
> mkl library on PC-Linux SUSE 10.0. After the installation, execution of
> sander gave me the following error message:
>
> sander: error while loading shared libraries: libvml.so: cannot open
> shared object file: No such file or directory
>
> Could someone please let me know how to troubleshoot this libvml.so problem.

Try compiling with the static flag:

 cd $AMBERHOME/src
 make clean
 configure -static ifort_x86_64 (and any other flags)
 make

OR add the directory where MKL keeps its libs (libvml.so) to the
LD_LIBRARY_PATH environment variable.

This is an example; you may need to adjust it to your situation

 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/opt/intel/mkl/8.0/lib"

regards,

Mark
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