Dear Amber Users,
I am trying to install a separate copy of Amber12+AmberTools13 to patch
plumed 1.3 for metadynamics study. I copied the installed directory
(/opt/amber12) to some other location. Then, I issued a "make clean
uninstall" command in /src and AmberTools/src directories.
After that I checked for mpif90, mpicc, mpiexec, using the following
commands with there results:
[root.leelab01 amber12]# which mpicc
/opt/mpi/intel-14.0/openmpi-1.6.5/bin/mpicc
[root.leelab01 amber12]# which mpiexec
/opt/mpi/intel-14.0/openmpi-1.6.5/bin/mpiexec
[root.leelab01 amber12]# mpif90 -show
ifort -I/opt/mpi/intel-14.0.3/openmpi-1.6.5/include
-I/opt/mpi/intel-14.0.3/openmpi-1.6.5/lib
-L/opt/mpi/intel-14.0.3/openmpi-1.6.5/lib -lmpi_f90 -lmpi_f77 -lmpi -ldl
-lm -lnuma -Wl,--export-dynamic -lrt -lnsl -lutil
[root.leelab01 amber12]# mpicc -show
icc -I/opt/mpi/intel-14.0.3/openmpi-1.6.5/include -pthread
-L/opt/mpi/intel-14.0.3/openmpi-1.6.5/lib -lmpi -ldl -lm -lnuma
-Wl,--export-dynamic -lrt -lnsl -lutil
Then run the ./configure command for parallel.
[root.leelab01 amber12]# ./configure -mpi gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 13 patches:
No patches available
Available Amber 12 patches:
No patches available
Searching for python2... Found python2.6: /usr/bin/python2.6
Obtaining the gnu suite version:
gcc -v
The version is 4.4.7
Testing the gcc compiler:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the gfortran compiler:
gfortran -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
testp.c
gfortran -O0 -c -o testp.f.o testp.f
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Configuring NetCDF (may be time-consuming)...
NetCDF configure succeeded.
Checking for zlib: OK
Checking for libbz2: OK
Configuring fftw-3.3 for mdgx (may be time-consuming)...
fftw-3.3 configure succeeded.
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
=======
Error comes while "make install" command:
csu-umbrella.F90(9): error #7013: This module file was not generated by any
release of this compiler. [NETCDF]
use netcdf, only : nf90_double, nf90_float
----^
ncsu-umbrella.F90(66): error #6592: This symbol must be a defined
parameter, an enumerator, or an argument of an inquiry function that
evaluates to a compile-time constant. [NF90_DOUBLE]
integer, private, parameter :: coeffs_type = nf90_double
---------------------------------------------^
ncsu-umbrella.F90(79): error #6592: This symbol must be a defined
parameter, an enumerator, or an argument of an inquiry function that
evaluates to a compile-time constant. [ONE]
double precision, private, parameter :: MINUS_ONE = -ONE
-----------------------------------------------------^
ncsu-umbrella.F90(80): error #6592: This symbol must be a defined
parameter, an enumerator, or an argument of an inquiry function that
evaluates to a compile-time constant. [ONE]
double precision, private, parameter :: ONE_THIRD = ONE/THREE
----------------------------------------------------^
ncsu-umbrella.F90(80): error #6592: This symbol must be a defined
parameter, an enumerator, or an argument of an inquiry function that
evaluates to a compile-time constant. [THREE]
double precision, private, parameter :: ONE_THIRD = ONE/THREE
--------------------------------------------------------^
ncsu-umbrella.F90(82): error #6592: This symbol must be a defined
parameter, an enumerator, or an argument of an inquiry function that
evaluates to a compile-time constant. [ONE]
double precision, private, parameter :: ONE_SIXTH = ONE/6
----------------------------------------------------^
ncsu-umbrella.F90(83): error #6592: This symbol must be a defined
parameter, an enumerator, or an argument of an inquiry function that
evaluates to a compile-time constant. [TWO]
double precision, private, parameter :: TWO_THIRD = TWO/THREE
----------------------------------------------------^
ncsu-umbrella.F90(83): error #6592: This symbol must be a defined
parameter, an enumerator, or an argument of an inquiry function that
evaluates to a compile-time constant. [THREE]
double precision, private, parameter :: TWO_THIRD = TWO/THREE
--------------------------------------------------------^
ncsu-umbrella.F90(84): error #6592: This symbol must be a defined
parameter, an enumerator, or an argument of an inquiry function that
evaluates to a compile-time constant. [ONE]
double precision, private, parameter :: HALF = ONE/TWO
-----------------------------------------------^
ncsu-umbrella.F90(84): error #6592: This symbol must be a defined
parameter, an enumerator, or an argument of an inquiry function that
evaluates to a compile-time constant. [TWO]
double precision, private, parameter :: HALF = ONE/TWO
---------------------------------------------------^
ncsu-umbrella.F90(795): error #7013: This module file was not generated by
any release of this compiler. [NETCDF]
use netcdf
-------^
ncsu-umbrella.F90(9): error #6580: Name in only-list does not exist.
[NF90_DOUBLE]
use netcdf, only : nf90_double, nf90_float
-------------------^
ncsu-umbrella.F90(9): error #6580: Name in only-list does not exist.
[NF90_FLOAT]
use netcdf, only : nf90_double, nf90_float
--------------------------------^
ncsu-umbrella.F90(12): error #6580: Name in only-list does not exist.
[ZERO]
use ncsu_constants, only : ZERO, ONE, TWO, THREE, FOUR
---------------------------^
ncsu-umbrella.F90(12): error #6580: Name in only-list does not exist.
[ONE]
use ncsu_constants, only : ZERO, ONE, TWO, THREE, FOUR
---------------------------------^
ncsu-umbrella.F90(12): error #6580: Name in only-list does not exist.
[TWO]
use ncsu_constants, only : ZERO, ONE, TWO, THREE, FOUR
--------------------------------------^
ncsu-umbrella.F90(12): error #6580: Name in only-list does not exist.
[THREE]
use ncsu_constants, only : ZERO, ONE, TWO, THREE, FOUR
-------------------------------------------^
ncsu-umbrella.F90(12): error #6580: Name in only-list does not exist.
[FOUR]
use ncsu_constants, only : ZERO, ONE, TWO, THREE, FOUR
--------------------------------------------------^
ncsu-umbrella.F90(122): error #6404: This name does not have a type, and
must have an explicit type. [ZERO]
if (.not.(spacing(n).gt.ZERO)) call afailed("ncsu-umbrella.F90", 122)
------------------------------^
ncsu-umbrella.F90(351): error #6404: This name does not have a type, and
must have an explicit type. [ONE]
hill = SCALE*(x2 - ONE)**2
-----------------------^
ncsu-umbrella.F90(811): error #6404: This name does not have a type, and
must have an explicit type. [NF90_NOWRITE]
rc = nf90_open(filename, nf90_nowrite, setid)
----------------------------^
ncsu-umbrella.F90(811): error #6404: This name does not have a type, and
must have an explicit type. [NF90_OPEN]
rc = nf90_open(filename, nf90_nowrite, setid)
--------^
ncsu-umbrella.F90(814): error #6404: This name does not have a type, and
must have an explicit type. [NF90_GLOBAL]
rc = nf90_get_att(setid, nf90_global, 'nextents', nextents)
----------------------------^
ncsu-umbrella.F90(814): error #6404: This name does not have a type, and
must have an explicit type. [NF90_GET_ATT]
rc = nf90_get_att(setid, nf90_global, 'nextents', nextents)
--------^
ncsu-umbrella.F90(818): error #6406: Conflicting attributes or multiple
declaration of name. [ERR_UNIT]
write (unit = ERR_UNIT, fmt = '(/a,a,a,a,'//pfmt(nextents)//',a/)') &
--------------------^
ncsu-umbrella.F90(818): error #6404: This name does not have a type, and
must have an explicit type. [PFMT]
write (unit = ERR_UNIT, fmt = '(/a,a,a,a,'//pfmt(nextents)//',a/)') &
--------------------------------------------------^
ncsu-umbrella.F90(818): error #6054: A CHARACTER data type is required in
this context. [PFMT]
write (unit = ERR_UNIT, fmt = '(/a,a,a,a,'//pfmt(nextents)//',a/)') &
--------------------------------------------------^
ncsu-umbrella.F90(845): error #6406: Conflicting attributes or multiple
declaration of name. [ERR_UNIT]
write (unit = ERR_UNIT, fmt = '(/a,a,a,a,i1,a,i1/)') ' **
NCSU-Error ** : ', &
-----------------------^
ncsu-umbrella.F90(851): error #6406: Conflicting attributes or multiple
declaration of name. [ERR_UNIT]
write (unit = ERR_UNIT, fmt = '(/a,a,a,a,i1,a/)') ' ** NCSU-Error
** : ', &
-----------------------^
ncsu-umbrella.F90(863): error #6404: This name does not have a type, and
must have an explicit type. [NF90_INQ_DIMID]
rc = nf90_inq_dimid(setid, 'row-major', dimid)
--------^
/tmp/ifortrLxNaj.i90(3796): catastrophic error: Too many errors, exiting
compilation aborted for ncsu-umbrella.F90 (code 1)
make[2]: *** [ncsu-umbrella.o] Error 1
make[2]: Leaving directory `/home/Bharat/Documents/amber12/src/sander'
make[1]: *** [parallel] Error 2
make[1]: Leaving directory `/home/Bharat/Documents/amber12/src'
make: *** [install] Error 2
Can anybody please help me to rectify this error?
--
*Best Regards*
Bharat
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Received on Tue Jul 05 2016 - 06:30:02 PDT
