Hi Ross,
Thanks for the tip. That seems to have worked well enough. I hope it can be
solved with not too much effort!
One thing I forgot to mention which may be relevant: when I was patching
stuff, I did get a message while applying bugfix.all that some patches
couldn't be applied. This was not a problem for bugfix_at.all. Does that
mean it's possible that because the part of the file where qmmm_div was to
be created had been modified away from that expected by the diff, that it
panicked and didn't do anything?
I can't recall which are the affected files now, and I think I may get
misleading results if I try to run the patch again on already patched
source. So I'll need to leave that up to you, but I hope that helps.
Cheers,
Ben
On 4/3/09 11:36 a.m., "Ross Walker" <ross.rosswalker.co.uk> wrote:
> Hi Ben,
>
> Let me take a look at this. In the meantime as a workaround, (assuming you
> don't want to use the Divcon QMMM (idc>0) - all other QMMM support will
> still be there) then you can add '-nosanderidc' to the configure_amber line.
> Make clean and then recompile and it should compile cleanly this time.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
>> Behalf Of Benjamin Roberts
>> Sent: Wednesday, March 04, 2009 7:48 AM
>> To: AMBER Mailing List
>> Subject: [AMBER] Compilation and qmmm_div
>>
>> Hi all,
>>
>> To make sure I have the most up-to-date version of Amber 10, I downloaded
>> a
>> copy of the Amber 10 release (from the CVS tree) then applied the patches
>> bugfix.all and bugfix_at.all, using the specified patch command. The
>> patches
>> apparently proceeded with no problems. However, when it comes time to
>> compile, I issue the command
>>
>> [user.computer src]$ make -f Makefile serial
>>
>> and get the following responses:
>>
>> Using ifort on Linux:
>> ---------------------
>> ---------------------
>>
>> ifort -c -w95 -vec_report0 -mp1 -O0 -FR -I../../sander -I../src/include
>> -DHAS_LAPACK -DQMMM -o ../obj/freq_qmmm.o ../src/freq/freq.F90
>> fortcom: Error: ../src/freq/freq.F90, line 11: Name in only-list does not
>> exist.
>> [QMMM_DIV]
>> use qmmm_module, only: qmmm_struct, qmmm_div
>> ---------------------------------------^
>> fortcom: Error: ../src/freq/freq.F90, line 38: The structure-name is
>> invalid
>> or is missing.
>> dimension dcl(3,qmmm_div%ntotatm+qmmm_struct%nlink)
>> ------------------^
>> fortcom: Error: ../src/freq/freq.F90, line 38: A specification expression
>> object must be a dummy argument, a COMMON block object, or an object
>> accessible through host or use association [QMMM_DIV]
>> dimension dcl(3,qmmm_div%ntotatm+qmmm_struct%nlink)
>> ------------------^
>>
>>
>>
>> Using gfortran on Mac:
>> ----------------------
>> ----------------------
>>
>> gfortran -c -O0 -fno-range-check -fno-second-underscore -ffree-form
>> -I../../sander -I../src/include -DHAS_LAPACK -DQMMM -o ../obj/freq_qmmm.o
>> ../src/freq/freq.F90
>> ../src/freq/freq.F90:11.38:
>>
>> use qmmm_module, only: qmmm_struct, qmmm_div
>> 1
>> Error: Symbol 'qmmm_div' referenced at (1) not found in module
>> 'qmmm_module'
>> ../src/freq/freq.F90:38.26:
>>
>> dimension dcl(3,qmmm_div%ntotatm+qmmm_struct%nlink)
>> 1
>> Error: Expected another dimension in array declaration at (1)
>>
>>
>> Whereupon in either case the compilation is immediately aborted.
>>
>> It looks to me as though a necessary declaration for qmmm_div is missing.
>> Could someone (perhaps the authors of the relevant QM/MM changes) tell me
>> where such a declaration is to be added? Thanks!
>>
>> Best regards,
>>
>> Ben
>>
>> --
>> Benjamin P. Roberts
>> Postdoctoral Research Associate
>> Quantum Theory Project
>> University of Florida
>>
>> 2301 New Physics Building #92
>> PO Box 118435
>> Gainesville FL 32611-8435
>> USA
>>
>> Phone: +1 352 392 6712
>> Cell: +1 352 222 3677
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Benjamin P. Roberts
Postdoctoral Research Associate
Quantum Theory Project
University of Florida
2301 New Physics Building #92
PO Box 118435
Gainesville FL 32611-8435
USA
Phone: +1 352 392 6712
Cell: +1 352 222 3677
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Received on Fri Mar 06 2009 - 01:15:26 PST
