Hi Ray,
It's not about whether you compiled in that folder - it is whether you maybe edited files in that folder that you never committed / pushed. Try doing:
git clean -f -d -x
git status
And see what it reports.
All the best
Ross
> On Feb 16, 2016, at 23:04, Ray Luo <rluo.uci.edu> wrote:
>
> Hi Ross,
>
> Yes, I think my folder is clean since I have never compiled anything
> in my amber git folder. Every time after syncing with the master
> branch, I copy the whole master branch to a new folder for compiling
> and testing.
>
> I'm about to test this evening's synced version, but will do "git
> clean -fxd" before configuring/compiling. Maybe this is why.
>
> By the way, could you add my uci email to the mailing list as well,
> i.e. "ray.luo.uci.edu"?
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Tue, Feb 16, 2016 at 7:51 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>> Hi Ray,
>>
>> If I do this - on my OSX laptop (GCC 4.9.3), MPICH version 3.1.4
>>
>> git pull
>> git clean -f -d -x
>> git status
>> On branch master
>> Your branch is up-to-date with 'origin/master'.
>> nothing to commit, working directory clean
>>
>> ./configure -mpi gnu
>> make install
>>
>> ...
>> ...
>> dnrm2.F90:113.24:
>>
>> ASSIGN 110 TO NEXT
>> 1
>> Warning: Deleted feature: ASSIGN statement at (1)
>> mpif90 -DBINTRAJ -DEMIL -DMPI -c -O3 -mtune=native -fPIC -ffree-form -I/Users/rcw/amber/amber/include -I/Users/rcw/amber/amber/include -o dcopy.o dcopy.F90
>> mpif90 -DBINTRAJ -DEMIL -DMPI -c -O3 -mtune=native -fPIC -ffree-form -I/Users/rcw/amber/amber/include -I/Users/rcw/amber/amber/include -o pb_force.o pb_force.F90
>> pb_force.F90:292.77:
>>
>> sa_init, sa_driver, sa_free, sa_free_mb, &
>> 1
>> Error: Symbol 'saslave_init' referenced at (1) not found in module 'solvent_accessibility'
>> make[3]: *** [pb_force.o] Error 1
>> make[2]: *** [libpbsa] Error 2
>> make[1]: *** [parallel] Error 2
>> make: *** [install] Error 2
>>
>> Same problem. Are you sure you have the latest tree and it is clean and doesn't have any modified files locally or files you forgot to add?
>>
>> All the best
>> Ross
>>
>>
>>> On Feb 16, 2016, at 15:56, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>>>
>>> Hi Ross,
>>>
>>> So far I can "configure -mpi gnu", "make install", and can also pass
>>> "make sander.BASIC.MPI". I'm running "make test.parallel.MM". I'm
>>> using "mpirun -np 4" for the mpi jobs. This is on Rocks 6.1/Centos
>>> 6.1. Which step was the problem?
>>>
>>> However I disabled "pbsa_mbfocus" in AmberTools/test/ since I'm in the
>>> process of removing this feature to accommodate incoming CUDA. I also
>>> need to update the test cases for sander/nab/mmpbsa ... which will be
>>> partially in today for sander/nab. I'm trying to get mmpbsa.py to work
>>> with the new python environment.
>>>
>>> All the best,
>>> Ray
>>> --
>>> Ray Luo, Ph.D.
>>> Professor
>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>> Chemical and Biomedical Engineering
>>> University of California, Irvine, CA 92697-3900
>>>
>>>
>>> On Tue, Feb 16, 2016 at 10:21 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>>>> Hi Ross,
>>>>
>>>> I'm looking into this ... There was a major overhaul of the code in
>>>> addition to new features in the last check in.
>>>>
>>>> All the best,
>>>>
>>>> Ray
>>>>
>>>> --
>>>> Ray Luo, Ph.D.
>>>> Professor
>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>>> Chemical and Biomedical Engineering
>>>> University of California, Irvine, CA 92697-3900
>>
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Received on Tue Feb 16 2016 - 20:30:03 PST
