AMBER Archive (2008)

Subject: Re: AMBER: AMBER10 Compilation (SGI Altix)

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Tue Sep 16 2008 - 11:56:45 CDT

Hi Ross:
Thank you for your response. I try to compile with ifort and all the test
fail. This is strange because I compile AMBER 8 with this compilers without
problem. I will update the icc ifort and mkl to v 10.

Cheers,

Anthony

On Monday 15 September 2008 10:15:54 pm Ross Walker wrote:
> Hi Anthony,
>
> This is not good... :-(. Can you try compiling in serial with the ifort
> target and see what happens there. It is really strange that you see all
> the NaN's etc, this normally means some kind of memory corruption, the sort
> of thing you'd see calling a 32 bit library from a 64 bit routine for
> example, although one would normally expect some kind of segfault here. The
> compiler shouldn't let you do this though.
>
> Thus more likely there is a routine, probably in the dihedral code, that is
> being misvectorized by the compiler. My first suggestion would be to try
> upgrading to the version 10 compilers if you can and see if this fixes it.
> If you can't do that or it is difficult, then try editing config_amber.h
> and changing the FFLAGS and FOPTFLAGS lines so they don't do any
> optimization (-O0) and remove any -axW etc flags, then make clean and
> recompile. If this works then it is a case of trying to track down which
> routine is causing the compiler problem, my first guess would be ephi.f
> and/or extra_pts.f in which case you could edit the Makefile so these are
> compiled with FFLAGS instead of FOPTFLAGS (and recreate config_amber.h by
> re-running configure_amber) and see if this helps, again make clean before
> building.
>
> Let us know how things go - hopefully just upgrading the compilers will fix
> the problem.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of Anthony Cruz
> > Sent: Monday, September 15, 2008 11:22 AM
> > To: amber_at_scripps.edu
> > Subject: AMBER: AMBER10 Compilation (SGI Altix)
> >
> > Hi Users:
> > Today I try to compile AMBER10 on a SGI Altix (uname -a : Linux gelato
> > 2.6.5-7.283-sn2 #1 SMP Wed Nov 29 16:55:53 UTC 2006 ia64 ia64 ia64
> > GNU/Linux)
> > To configure I use sgi_altix option (icc v 9.0 , ifort v9.0 , MKL v9.0).
> > It
> > seems to compile without error but all the test fail. Also some of the
> > test
> > from amber tools fail. I check the netcdf (make check) and pass all test.
> > Here is the output for the test.serial (TEST_FAILURES.diff):
> >
> > possible FAILURE: check mdout.dmp.dif
> > /tmp/amber/amber10/test/dmp
> > 67,68c67,68
> > < 1 -4.2572E+1 1.2493E+1 5.6294E+1 P8 6
> > < BOND = 0.7921 ANGLE = 2.0379 DIHED =
> > 0.7121
> > ---
> >
> > > 1 -4.2573E+1 1.2492E+1 5.6291E+1 P8 6
> > > BOND = 0.7921 ANGLE = 2.0379 DIHED =
> >
> > 0.7120
> > 74,75c74,75
> > < 2 -4.2582E+1 1.2460E+1 5.6128E+1 P8 6
> > < BOND = 0.7874 ANGLE = 2.0325 DIHED =
> > 0.7121
> > ---
> >
> > > 2 -4.2582E+1 1.2459E+1 5.6125E+1 P8 6
> > > BOND = 0.7874 ANGLE = 2.0325 DIHED =
> >
> > 0.7120
> > 81,82c81,82
> > < 3 -4.2593E+1 1.2420E+1 5.5930E+1 P8 6
> > < BOND = 0.7817 ANGLE = 2.0260 DIHED =
> > 0.7120
> > ---
> >
> > > 3 -4.2593E+1 1.2420E+1 5.5927E+1 P8 6
> > > BOND = 0.7817 ANGLE = 2.0260 DIHED =
> >
> > 0.7119
> > 88,89c88,89
> > < 4 -4.2606E+1 1.2373E+1 5.5692E+1 P8 6
> > < BOND = 0.7750 ANGLE = 2.0182 DIHED =
> > 0.7119
> > ---
> >
> > > 4 -4.2606E+1 1.2373E+1 5.5689E+1 P8 6
> > > BOND = 0.7750 ANGLE = 2.0182 DIHED =
> >
> > 0.7118
> > 95,96c95,96
> > < 5 -4.2622E+1 1.2317E+1 5.5407E+1 P8 6
> > < BOND = 0.7669 ANGLE = 2.0089 DIHED =
> > 0.7117
> > ---
> >
> > > 5 -4.2622E+1 1.2316E+1 5.5404E+1 P8 6
> > > BOND = 0.7669 ANGLE = 2.0089 DIHED =
> >
> > 0.7116
> > 104,105c104,105
> > < 5 -4.2622E+1 1.2317E+1 5.5407E+1 P8 6
> > < BOND = 0.7669 ANGLE = 2.0089 DIHED =
> > 0.7117
> > ---
> >
> > > 5 -4.2622E+1 1.2316E+1 5.5404E+1 P8 6
> > > BOND = 0.7669 ANGLE = 2.0089 DIHED =
> >
> > 0.7116
> > ---------------------------------------
> > possible FAILURE: check mdout.adenine.dif
> > /tmp/amber/amber10/test/adenine
> > 69,70c69,70
> > < 1 1.4956 4.7935 2.7454E+1 N3 25
> > < BOND = 0.4545 ANGLE = 5.3215 DIHED =
> > 17.5374
> > ---
> >
> > > 1 1.5174 4.7855 2.7453E+1 N3 25
> > > BOND = 0.4545 ANGLE = 5.3215 DIHED =
> >
> > 17.5592
> > 76,77c76,77
> > < 2 1.2908 3.4147 1.7746E+1 N3 25
> > < BOND = 0.4346 ANGLE = 5.1757 DIHED =
> > 17.5358
> > ---
> >
> > > 2 NaN NaN 0. H5T 1
> > > BOND = 0.4346 ANGLE = 5.1751 DIHED = NaN
> >
> > 79c79
> > < 1-4 VDW = 7.1923 1-4 EEL = 6.1795 RESTRAINT =
> > 0.
> > ---
> >
> > > 1-4 VDW = 7.1922 1-4 EEL = 6.1795 RESTRAINT =
> >
> > 0.
> > 83,137c83,137
> > < 3 1.1266 2.1977 9.9540 N3 25
> > < BOND = 0.4585 ANGLE = 5.0362 DIHED =
> > 17.5348
> > < VDWAALS = -3.6387 EEL = -24.8259 HBOND =
> > 0.
> > < 1-4 VDW = 7.1691 1-4 EEL = 6.1467 RESTRAINT =
> > 0.
> > < EPOLAR = -6.7540
> > < Dipole convergence: rms = 0.258E-6 iters = 3.00
> > < NSTEP ENERGY RMS GMAX NAME
> > NUMBER
> > < 4 1.0010 1.6429 7.4065 EP23 26
> > < BOND = 0.4942 ANGLE = 4.9350 DIHED =
> > 17.5342
> > < VDWAALS = -3.6421 EEL = -24.7961 HBOND =
> > 0.
> > < 1-4 VDW = 7.1421 1-4 EEL = 6.0892 RESTRAINT =
> > 0.
> > < EPOLAR = -6.7554
> > < Dipole convergence: rms = 0.659E-6 iters = 3.00
> > < NSTEP ENERGY RMS GMAX NAME
> > NUMBER
> > < 5 9.2259E-1 3.1051 1.3689E+1 EP23 26
> > < BOND = 0.4804 ANGLE = 4.9120 DIHED =
> > 17.5322
> > < VDWAALS = -3.6456 EEL = -24.7132 HBOND =
> > 0.
> > < 1-4 VDW = 7.1263 1-4 EEL = 5.9910 RESTRAINT =
> > 0.
> > < EPOLAR = -6.7605
> > < Dipole convergence: rms = 0.766E-6 iters = 3.00
> > < NSTEP ENERGY RMS GMAX NAME
> > NUMBER
> > < 6 1.1652 8.9082 4.6701E+1 N3 25
> > < BOND = 0.4929 ANGLE = 5.1589 DIHED =
> > 17.5309
> > < VDWAALS = -3.6507 EEL = -24.7333 HBOND =
> > 0.
> > < 1-4 VDW = 7.1146 1-4 EEL = 6.0155 RESTRAINT =
> > 0.
> > < EPOLAR = -6.7637
> > < Dipole convergence: rms = 0.269E-6 iters = 4.00
> > < NSTEP ENERGY RMS GMAX NAME
> > NUMBER
> > < 7 8.6292E-1 2.7405 1.4587E+1 N3 25
> > < BOND = 0.4660 ANGLE = 4.8797 DIHED =
> > 17.5307
> > < VDWAALS = -3.6498 EEL = -24.7002 HBOND =
> > 0.
> > < 1-4 VDW = 7.1191 1-4 EEL = 5.9808 RESTRAINT =
> > 0.
> > < EPOLAR = -6.7633
> > < Dipole convergence: rms = 0.365E-6 iters = 4.00
> > < NSTEP ENERGY RMS GMAX NAME
> > NUMBER
> > < 8 8.9665E-1 4.6266 2.1383E+1 N3 25
> > < BOND = 0.4635 ANGLE = 4.9140 DIHED =
> > 17.5299
> > < VDWAALS = -3.6499 EEL = -24.6488 HBOND =
> > 0.
> > < 1-4 VDW = 7.1229 1-4 EEL = 5.9289 RESTRAINT =
> > 0.
> > < EPOLAR = -6.7640
> > < Dipole convergence: rms = 0.348E-6 iters = 3.00
> > < NSTEP ENERGY RMS GMAX NAME
> > NUMBER
> > < 9 8.0872E-1 1.2342 5.5340 EP23 26
> > < BOND = 0.4542 ANGLE = 4.8390 DIHED =
> > 17.5297
> > < VDWAALS = -3.6511 EEL = -24.6601 HBOND =
> > 0.
> > < 1-4 VDW = 7.1201 1-4 EEL = 5.9415 RESTRAINT =
> > 0.
> > < EPOLAR = -6.7647
> > < Dipole convergence: rms = 0.180E-6 iters = 4.00
> > < NSTEP ENERGY RMS GMAX NAME
> > NUMBER
> > < 10 7.9896E-1 2.3141 1.2573E+1 N3 25
> > < BOND = 0.4486 ANGLE = 4.8418 DIHED =
> > 17.5287
> > < VDWAALS = -3.6535 EEL = -24.6493 HBOND =
> > 0.
> > < 1-4 VDW = 7.1163 1-4 EEL = 5.9331 RESTRAINT =
> > 0.
> > < EPOLAR = -6.7666
> > < Dipole convergence: rms = 0.436E-6 iters = 3.00
> > ---
> >
> > > 3 NaN NaN 0. H5T 1
> > > BOND = NaN ANGLE = NaN DIHED = NaN
> > > VDWAALS = 0. EEL = 0. HBOND = 0.
> > > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> >
> > 0.
> >
> > > EPOLAR = NaN
> > > Dipole convergence: rms = NaN iters = 21.00
> > > NSTEP ENERGY RMS GMAX NAME
> >
> > NUMBER
> >
> > > 4 NaN NaN 0. H5T 1
> > > BOND = NaN ANGLE = NaN DIHED = NaN
> > > VDWAALS = 0. EEL = 0. HBOND = 0.
> > > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> >
> > 0.
> >
> > > EPOLAR = NaN
> > > Dipole convergence: rms = NaN iters = 21.00
> > > NSTEP ENERGY RMS GMAX NAME
> >
> > NUMBER
> >
> > > 5 NaN NaN 0. H5T 1
> > > BOND = NaN ANGLE = NaN DIHED = NaN
> > > VDWAALS = 0. EEL = 0. HBOND = 0.
> > > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> >
> > 0.
> >
> > > EPOLAR = NaN
> > > Dipole convergence: rms = NaN iters = 21.00
> > > NSTEP ENERGY RMS GMAX NAME
> >
> > NUMBER
> >
> > > 6 NaN NaN 0. H5T 1
> > > BOND = NaN ANGLE = NaN DIHED = NaN
> > > VDWAALS = 0. EEL = 0. HBOND = 0.
> > > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> >
> > 0.
> >
> > > EPOLAR = NaN
> > > Dipole convergence: rms = NaN iters = 21.00
> > > NSTEP ENERGY RMS GMAX NAME
> >
> > NUMBER
> >
> > > 7 NaN NaN 0. H5T 1
> > > BOND = NaN ANGLE = NaN DIHED = NaN
> > > VDWAALS = 0. EEL = 0. HBOND = 0.
> > > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> >
> > 0.
> >
> > > EPOLAR = NaN
> > > Dipole convergence: rms = NaN iters = 21.00
> > > NSTEP ENERGY RMS GMAX NAME
> >
> > NUMBER
> >
> > > 8 NaN NaN 0. H5T 1
> > > BOND = NaN ANGLE = NaN DIHED = NaN
> > > VDWAALS = 0. EEL = 0. HBOND = 0.
> > > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> >
> > 0.
> >
> > > EPOLAR = NaN
> > > Dipole convergence: rms = NaN iters = 21.00
> > > NSTEP ENERGY RMS GMAX NAME
> >
> > NUMBER
> >
> > > 9 NaN NaN 0. H5T 1
> > > BOND = NaN ANGLE = NaN DIHED = NaN
> > > VDWAALS = 0. EEL = 0. HBOND = 0.
> > > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> >
> > 0.
> >
> > > EPOLAR = NaN
> > > Dipole convergence: rms = NaN iters = 21.00
> > > NSTEP ENERGY RMS GMAX NAME
> >
> > NUMBER
> >
> > > 10 NaN NaN 0. H5T 1
> > > BOND = NaN ANGLE = NaN DIHED = NaN
> > > VDWAALS = 0. EEL = 0. HBOND = 0.
> > > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> >
> > 0.
> >
> > > EPOLAR = NaN
> > > Dipole convergence: rms = NaN iters = 21.00
> >
> > 141,146c141,146
> > < 10 7.9896E-1 2.3141 1.2573E+1 N3 25
> > < BOND = 0.4486 ANGLE = 4.8418 DIHED =
> > 17.5287
> > < VDWAALS = -3.6535 EEL = -24.6493 HBOND =
> > 0.
> > < 1-4 VDW = 7.1163 1-4 EEL = 5.9331 RESTRAINT =
> > 0.
> > < EPOLAR = -6.7666
> > < Dipole convergence: rms = 0.436E-6 iters = 3.00
> > ---
> >
> > > 10 NaN NaN 0. H5T 1
> > > BOND = NaN ANGLE = NaN DIHED = NaN
> > > VDWAALS = 0. EEL = 0. HBOND = 0.
> > > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> >
> > 0.
> >
> > > EPOLAR = NaN
> > > Dipole convergence: rms = NaN iters = 21.00
> >
> > ---------------------------------------
> >
> > What could be the problem?
> >
> > Cheers,
> >
> > Anthony
> > -----------------------------------------------------------------------
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> > To post, send mail to amber_at_scripps.edu
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> > to majordomo_at_scripps.edu
>
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