AMBER Archive (2009)

Subject: [AMBER] amber10 installation problem

From: Lan JIN (lansingmy_at_yahoo.com.cn)
Date: Wed Jul 08 2009 - 01:49:05 CDT

Hello there,

I have been trying to install Amber10 and AmberTool
1.2 on my Linux (Intel core2, RHEL4, 32 bit) computer. Bugfix files for
both were downloaded and 'patch' did as well.

My first
question is if these two packages are totally independent during
installation or failure of AmberTool installation will affect the
installation of AMBER10. 

========for AmberTool1.2=============

configure_at
gcc worked well as follows but config.h (not edited) returned with
errors. I also tried to edit config.h file by changing to FC=ifort from
g77 and FFLAGS variables but without any difference.

> ./configure_at gcc
Setting AMBERHOME to /usr/local/AMBER/amber10

Using Intel MKL libraries in /opt/intel/mkl/10.1.1.019

Testing the C compiler:
      gcc  -m32 -o testp
 testp.c
OK

Obtaining the C++ compiler version:
      g++ -v
The version is 3.4.6
OK

Testing the g77 compiler:
     g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
OK

Testing flex:
OK

Configuring netcdf; (may be time-consuming)

NETCDF configure succeeded.

The configuration file, config.h, was successfully created.

The next step is to type 'make -f Makefile_at'

> make -f Makefile_at

.............
.............
xyzint.o(.text+0x266): In function `xyzint_':
: undefined reference to `__intel_cpu_indicator'
xyzint.o(.text+0x275): In function `xyzint_':
: undefined reference to `__intel_cpu_indicator_init'
xyzint.o(.text+0x5c4): In function `xyzint_.J':
: undefined reference to `__libm_sse2_acos'
xyzint.o(.text+0xd58): In function `xyzgeo_.':
: undefined reference to
 `__intel_cpu_indicator'
xyzint.o(.text+0xd68): In function `xyzgeo_.':
: undefined reference to `__intel_cpu_indicator'
xyzint.o(.text+0xd77): In function `xyzgeo_.':
: undefined reference to `__intel_cpu_indicator_init'
xyzint.o(.text+0xf5c): In function `xyzgeo_.J':
: undefined reference to `__libm_sse2_acos'
xyzint.o(.text+0x10df): In function `xyzgeo_.J':
: undefined reference to `__libm_sse2_acos'
xyzint.o(.text+0x1453): In function `xyzgeo_.J':
: undefined reference to `__libm_sse2_acos'
collect2: ld returned 1 exit status
make[1]: *** [mopac] error 1
make[1]: Leaving directory `/usr/local/AMBER/amber10/src/mopac6/src'
make: *** [install] error 2

'make -f Makefile_at test' stopped at 

..............
..............
Running test of fibre-diffraction module

sh: /usr/local/AMBER/amber10/bin/teLeap: no such file or directory
getpdb: can't open file
 nab_tmp.pdb.lpdb
make[1]: *** [fd_test] error 1
make[1]: Leaving directory `/usr/local/AMBER/amber10/test/nab'
make: *** [test.nab] error 2

======================for Amber10====================

I continued to install Amber10 assuming the AmberTool would not affect this process.

> ./configure_amber ifort
> make serial
> make clean

> make test

.............
cd bintraj && ./Run.bintraj
../../src/netcdf/bin/ncdump: Command not found.
diffing nc_headers.save with nc_headers
possible FAILURE:  check nc_headers.dif
...............

> make test.serial.QMMM

..........
cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma
DFTB SLKO files not found - Skipping Test...

cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md
DFTB SLKO files not found - Skipping Test...

cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb0
DFTB SLKO files
 not found - Skipping Test...
..............
.............
..........
cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_qmewald2
DFTB SLKO files not found - Skipping Test...

cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb2
DFTB SLKO files not found - Skipping Test...

diffing divcon.out.save with divcon.out
possible FAILURE:  check divcon.out.dif

The TEST_FAILURES.diff file is pasted below.

possible FAILURE:  check nc_headers.dif
/usr/local/AMBER/amber10/test/bintraj
1,31d0
< netcdf mdtrj {
< dimensions:
<       frame = UNLIMITED ; // (10 currently)
<       spatial = 3 ;
<       atom = 28 ;
<       label = 5 ;
<       cell_spatial = 3
 ;
<       cell_angular = 3 ;
< variables:
<       char spatial(spatial) ;
<       float time(frame) ;
<               time:units = "picosecond" ;
<       float coordinates(frame, atom, spatial) ;
<               coordinates:units = "angstrom" ;
<       char cell_spatial(cell_spatial) ;
<       char cell_angular(cell_angular, label) ;
<       double cell_lengths(frame, cell_spatial) ;
<               cell_lengths:units = "angstrom" ;
<      
 double cell_angles(frame, cell_angular) ;
<               cell_angles:units = "degree" ;
<       float velocities(frame, atom, spatial) ;
<               velocities:units = "angstrom/picosecond" ;
<               velocities:scale_factor = 20.455f ;
< // global attributes:
<               :title = "netCDF output test" ;
<               :application = "AMBER" ;
<               :program = "sander"
 ;
<               :programVersion = "10.0" ;
<               :Conventions = "AMBER" ;
<               :ConventionVersion = "1.0" ;
< }
---------------------------------------
possible FAILURE:  check divcon.out.dif
/usr/local/AMBER/amber10/test/water2_qmmmnmr
51c51
<        1         O            -0.00554     1.52120     0. 

---
>        1         O            -0.00554    
 1.52120     0.  RES
---------------------------------------

AmberTool
should be not installed. xleap, ptraj etc do not exist but antechamber
is there. I am a little bit confused with this. Please can anybody give
any suggestion about this? How can I check these problems and installed
the two packages successfully? 

Many thanks in advance.

Lan 

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