Jason,
The error should be from either MPI or netcdf setting, I think. The
compiling for parallel amber failed again with many error messages:
=======================================
Error: Syntax error in argument list at (1)
In file _memory_module.f:485
nmr_work => x(lnmr01:lnmr01+irlreq-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:486
nmr_iwork => ix(inmr02:inmr02+intreq-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:488
reff => x(l98:l98+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:489
onereff => x(l99:l99+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:491
gb_vdw_radii => x(l165:l165+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:492
gb_p1 => x(l170:l170+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:493
gb_p2 => x(l175:l175+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:494
gb_p3 => x(l180:l180+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:495
gb_p4 => x(l185:l185+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:496
rborn_max => x(l186:l186+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:497
rborn_min => x(l187:l187+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:498
rborn_ave => x(l188:l188+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:499
rborn_fluct => x(l189:l189+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:506
nmr_imet => ix(i65:i65+mxsub*isubi-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:507
nmr_xmet => x(l105:l105+mxsub*isubr-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:508
nmr_force => x(l110:l110+3*natom+mxvar-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:509
nmr_ddep => x(l115:l115+ma*ma-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:510
nmr_dddep => x(l120:l120+3*ma*ma-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:511
nmr_dorat => x(l125:l125+3*ma*ma-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:512
nmr_ddrat => x(l130:l130+3*ma*ma-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:513
nmr_rate => x(l135:l135+ma*ma-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:514
nmr_trp => x(l140:l140+ma*ma-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:515
nmr_dint => x(l145:l145+3*ma+mxvar-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:519
cnstph_dcharge => x(l190:l190+natom-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:520
cnstph_atom_chrg => x(lcpcrg:lcpcrg+1000-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:521
cnstph_titr_states => x(lcpene:lcpene+200-1)
1
Error: Syntax error in argument list at (1)
In file _memory_module.f:525
end subroutine memory_init
1
Error: Non-numeric character in statement label at (1)
In file _memory_module.f:525
end subroutine memory_init
1
Error: Unclassifiable statement at (1)
In file _memory_module.f:527
subroutine set_rank2_pointer(ptr,array,dim1,dim2)
1
Error: Non-numeric character in statement label at (1)
In file _memory_module.f:527
subroutine set_rank2_pointer(ptr,array,dim1,dim2)
1
Error: Unclassifiable statement at (1)
In file _memory_module.f:528
double precision, pointer :: ptr(:,:)
1
Error: Unexpected data declaration statement at (1)
In file _memory_module.f:529
integer, intent(in) :: dim1, dim2
1
Error: Unexpected data declaration statement at (1)
In file _memory_module.f:530
double precision, target :: array(dim1,dim2)
1
Error: Unexpected data declaration statement at (1)
In file _memory_module.f:532
end subroutine set_rank2_pointer
1
Error: Non-numeric character in statement label at (1)
In file _memory_module.f:532
end subroutine set_rank2_pointer
1
Error: Unclassifiable statement at (1)
In file _memory_module.f:534
end module memory_module
1
Error: Non-numeric character in statement label at (1)
In file _memory_module.f:534
end module memory_module
1
Error: Unclassifiable statement at (1)
Error: Unexpected end of file in '_memory_module.f'
make[1]: *** [memory_module.o] Error 1
make[1]: Leaving directory `/opt/amber11/src/sander'
make: *** [parallel] Error 2
=======================================
Any advice? Appreciations.
Regards,
Yubo
On Mon, 21 Jun 2010 16:29:43 -0400
Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> See my comments below.
>
> On Mon, Jun 21, 2010 at 4:25 PM, Yubo Fan
><yubofan.mail.chem.tamu.edu>wrote:
>
>> Dr. Case,
>>
>> I got a problem to compile parallel version of Amber on my local
>> machine. The commands and error message are shown below:
>>
>>
>> =================================================================================
>> [root.localhost src]# ./configure -mpi intel
>> Your AMBERHOME environment variable should be set to /opt/amber11
>>
>> Using Intel MKL libraries in
>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t
>> MKL Version 10 or 11 assumed.
>>
>> Testing the icc compiler:
>> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
>>testp.c
>> OK
>>
>> Testing the ifort compiler:
>> ifort -O0 -o testp testp.f
>> OK
>>
>> Testing mixed C/Fortran compilation:
>> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
>> testp.c
>> ifort -O0 -c -o testp.f.o testp.f
>> icc -o testp testp.c.o testp.f.o
>> -L/opt/intel/Compiler/11.1/072/lib/intel64/ -lifport -lifcore -lsvml
>> /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so: warning:
>>warning:
>> feupdateenv is not implemented and will always fail
>> OK
>>
>> Testing pointer size:
>> icc -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 Parallel NetCDF; (may be time-consuming)
>>
>> Error: parallel NetCDF configure returned 77
>> Parallel NetCDF configure failed! Check the pnetcdf/config.log
>> file.
No pnetcdf files found.
>>
>
> What does pnetcdf/config.log say?
>
>
>> Continuing but parallel NetCDF will be skipped.
>>
>> Configuring NetCDF; (may be time-consuming)
>>
>> NetCDF configure succeeded.
>>
>> Configuring fftw-2.1.5; (may be time-consuming)
>>
>> Error: fftw configure returned 1
>> fftw configure failed! Check the fftw2_config.log file.
>>
>
> What does this file say?
>
> It may be that you don't have a working MPI, or you're using a
>mis-match of
> MPIs. This is especially true for personal systems, since users may
>not
> have properly built their MPIs. What does "mpif90 -show" and "mpicc
>-show"
> return on your system?
mpif90 -show
gfortran -I/usr/local/include -pthread -I/usr/local/lib
-L/usr/local/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl
-Wl,--export-dynamic -lnsl -lutil -lm -ldl
mpicc
gcc -I/usr/local/include -pthread -L/usr/local/lib -lmpi -lopen-rte
-lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>
> Good luck!
> Jason
>
>
>>
>> =================================================================================
>>
>> Any advice?
>>
>> Regards,
>> Yubo
>>
>> On Mon, 14 Jun 2010 12:34:13 -0400
>> case <case.biomaps.rutgers.edu> wrote:
>> > On Mon, Jun 14, 2010, Yubo Fan wrote:
>> >>
>> >> When I ran 'make parallel' at $AMBERHOME/src, the error message
>> >> appears as:
>> >> Error: config.h is not of type parallel!
>> >> Rerun ./configure and specify an MPI implementation.
>> >> make: *** [configured_parallel] Error 2
>> >>
>> >> The making of AmberTools and 'make serial' passed already. I ran
>> >> './configure -openmp intel' to create a config.h file at
>> >
>> > This is wrong, although perhaps an understandable error.
>> >
>> > 1. AmberTools can be made in parallel in two ways: using openmp
>>or
>> >MPI.
>> >
>> > 2. However, Amber itself can only be made in parallel using MPI.
>> > So, from
>> > the point of view of Amber, using the "-openmp" option is not
>>enough
>> >to give
>> > a "parallel" config.h. You need to run the configure script using
>> >the "-mpi"
>> > option, not the "openmp" one.
>> >
>> > ....dac
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> Yubo Fan
>> Chemistry Department
>> Texas A & M University
>> Tel: (979) 845-5237
>> Email: yubofan.mail.chem.tamu.edu
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
Yubo Fan
Chemistry Department
Texas A & M University
Tel: (979) 845-5237
Email: yubofan.mail.chem.tamu.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 21 2010 - 17:30:03 PDT
