Hi All,
Thanks to Jarrod for giving me a login to his Altix.
Okay this is definately a compiler bug on the part of Intel. Here is the
effected code. The file is qm_link_atoms.f and I have inserted a few write
statements to output the value of nlink:
qmmm_struct%nlink=0
do i=1,nbona
ii = .false.
jj = .false.
do j=1,qmmm_struct%nquant
ii=ii .or. ((ib(i)/3 + 1).eq.qmmm_nml%iqmatoms(j))
jj=jj .or. ((jb(i)/3 + 1).eq.qmmm_nml%iqmatoms(j))
end do
if (ii .neqv. jj) then
write(6,*) "passed test nlink before=",qmmm_struct%nlink
qmmm_struct%nlink=qmmm_struct%nlink+1
write(6,*) "passed test nlink after=",qmmm_struct%nlink
end if
end do
write(6,*) "link atoms 3 nlink=",qmmm_struct%nlink
With ifort 8.1 this gives as expected:
passed test nlink before= 0
passed test nlink after= 1
passed test nlink before= 1
passed test nlink after= 2
passed test nlink before= 2
passed test nlink after= 3
passed test nlink before= 3
passed test nlink after= 4
passed test nlink before= 4
passed test nlink after= 5
passed test nlink before= 5
passed test nlink after= 6
passed test nlink before= 6
passed test nlink after= 7
passed test nlink before= 7
passed test nlink after= 8
link atoms 3 nlink= 8
But with ifort 9.1.040 on Altix this gives:
passed test nlink before= 0
passed test nlink after= 1
passed test nlink before= 1
passed test nlink after= 2
passed test nlink before= 2
passed test nlink after= 3
passed test nlink before= 3
passed test nlink after= 4
passed test nlink before= 3
passed test nlink after= 4
passed test nlink before= 3
passed test nlink after= 4
passed test nlink before= 3
passed test nlink after= 4
passed test nlink before= 3
passed test nlink after= 4
link atoms 3 nlink= 3
So after 4 iterations of the loop nlink gets hoplessly corrupted.
It looks like this is related to misoptimization of this file by the Intel
compiler. The following temporary workaround should work:
Edit $AMBERHOME/src/sander/depend
change (line 2566)
qm_link_atoms.o: qm_link_atoms.f
$(FPP) qm_link_atoms.f > _qm_link_atoms.f
$(FC) -c $(FOPTFLAGS) -o $. _qm_link_atoms.f
to
qm_link_atoms.o: qm_link_atoms.f
$(FPP) qm_link_atoms.f > _qm_link_atoms.f
$(FC) -c $(FOPTFLAGS) -O2 -o $. _qm_link_atoms.f
then cd $AMBERHOME/src/
make clean
make
cd ../test/
make
And this time it will hopefully work. Hopefully Intel will fix this in later
versions of their compiler so for the moment I won't try to put a formal
bugfix together for this as it could be tricky to work around this bug.
Let me know if you have any further problems.
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Sun Feb 25 2007 - 06:07:52 PST
