Hi again. Well, here we go:
On 4/30/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote: > Up to now, I could finally compile it with Portland, in both single and > double precision version. But, on the other hand, while the single > precision works properly, the double precision fails in some tests, like > the "mixed" test on the "tutor" directory. It yelds me the following > error message: this is hard to debug, but what you could do is run the same tpr with different executables and do gmxcheck -e -e2 to compare energies. that might give a clue. > step 0 > Step 1 Warning: pressure scaling more than 1%, mu: 1.01018 1.02193 1.08117 > Step 2 Warning: pressure scaling more than 1%, mu: 1.01124 1.00787 1.08362 > Step 143 Warning: pressure scaling more than 1%, mu: 1.00304 1.00017 1.01009 > step 240, remaining runtime: 40 s > Program mdrun_d, VERSION 3.3 > Source code file: stat.c, line: 283 > Fatal error: > XTC error
Ok, I did gmxcheck for both double precision versions of gromacs I got: one compiled with GCC, and the other with PGI. Here is what I got. Everything looks to be ugly and different, btw; no idea where to look first: ***************************************************************************************************************** comparing energy file ener.edr and ener2.edr Opened ener.edr as double precision energy file Opened ener2.edr as double precision energy file There are 44 terms in the energy files There are 44 terms to compare in the energy files Reading frame 1 time 0.000 Pressure (bar) step 0: 2.26575e+06, step 0: -1212.92 pV step 0: 3.53269e+06, step 0: -1891.14 Vir-XX step 0: -475104, step 0: 2135.61 Vir-XY step 0: 491116, step 0: -544.385 Vir-XZ step 0: 763516, step 0: 180.112 Vir-YX step 0: 491225, step 0: -544.385 Vir-YY step 0: -1.02488e+06, step 0: 2008.1 Vir-YZ step 0: -1.53177e+06, step 0: 558.876 Vir-ZX step 0: 763218, step 0: 180.112 Vir-ZY step 0: -1.53059e+06, step 0: 558.876 Vir-ZZ step 0: -3.79554e+06, step 0: 2209.48 Pres-XX (bar) step 0: 610883, step 0: -1286.57 Pres-XY (bar) step 0: -630004, step 0: 664.233 Pres-XZ (bar) step 0: -979427, step 0: -271.252 Pres-YX (bar) step 0: -630144, step 0: 664.233 Pres-YY (bar) step 0: 1.3161e+06, step 0: -1124.86 Pres-YZ (bar) step 0: 1.96481e+06, step 0: -753.997 Pres-ZX (bar) step 0: -979044, step 0: -271.252 Pres-ZY (bar) step 0: 1.9633e+06, step 0: -753.997 Pres-ZZ (bar) step 0: 4.87027e+06, step 0: -1227.32 #Surf*SurfTen step 0: 9.18092e+06, step 0: -50.7689 Reading frame 3 time 0.100 Angle step 50: 1570.43, step 50: 306.588 LJ (SR) step 50: -449.51, step 50: -188.033 Disper. corr. step 50: -48.4547, step 50: -193.09 Coulomb (SR) step 50: -1821.5, step 50: -14751.3 Potential step 50: -749.035, step 50: -14825.8 Kinetic En. step 50: 4695.12, step 50: 3702.53 Total Energy step 50: 3946.09, step 50: -11123.3 Temperature step 50: 402.631, step 50: 317.511 Pressure (bar) step 50: 35297.3, step 50: -836.341 Box-X step 50: 6.85856, step 50: 4.68882 Box-Y step 50: 3.81751, step 50: 2.34589 Box-Z step 50: 3.93067, step 50: 2.34792 Volume step 50: 102.915, step 50: 25.8259 Density (SI) step 50: 174.458, step 50: 695.211 pV step 50: 218762, step 50: -1300.74 Vir-XX step 50: -34277.1, step 50: 1588.65 Vir-XY step 50: -19728.5, step 50: 108.132 Vir-XZ step 50: -14866.4, step 50: 14.285 Vir-YX step 50: -20282.2, step 50: 108.132 Vir-YY step 50: -185709, step 50: 2157.54 Vir-YZ step 50: -102950, step 50: -196.053 Vir-ZX step 50: -15598.4, step 50: 14.285 Vir-ZY step 50: -102762, step 50: -196.053 Vir-ZZ step 50: -103462, step 50: 1907.44 Pres-XX (bar) step 50: 11541.9, step 50: -445.503 Pres-XY (bar) step 50: 6367.62, step 50: -183.086 Pres-XZ (bar) step 50: 4787.13, step 50: -18.5143 Pres-YX (bar) step 50: 6546.3, step 50: -183.086 Pres-YY (bar) step 50: 60435.8, step 50: -1150.69 Pres-YZ (bar) step 50: 33194.4, step 50: 289.951 Pres-ZX (bar) step 50: 5023.35, step 50: -18.5143 Pres-ZY (bar) step 50: 33133.8, step 50: 289.951 Pres-ZZ (bar) step 50: 33914.2, step 50: -912.829 #Surf*SurfTen step 50: -8154.99, step 50: -269.382 Pcoupl-Mu-YY step 50: 1.00103, step 50: 0.999981 Mu-X step 50: 3.81572, step 50: 6.43379 Mu-Y step 50: -28.1838, step 50: -29.6693 Mu-Z step 50: -17.7016, step 50: -12.1778 T-MeOH step 50: 448.795, step 50: 306.87 T-SOL step 50: 348.773, step 50: 329.927 Lamb-MeOH step 50: 0.997024, step 50: 0.999745 . . . Reading frame 10 time 0.500 End of file on ener.edr but not on ener2.edr *************************************************************************************************************** I'm sorry for posting such a big output here, but I had no idea what to select, and it is really starting to look like a not-yet documented issue, at least for the gromacs+pgi combination. Anyone with more experience on gmxcheck can help? Or did someone any time found this or a problem like this? Thanks a lot for all help already provided. :D Jones _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
