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AMBER Archive (2004)
Subject: RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
From: Mark Williamson (mark.williamson_at_imperial.ac.uk)
Date: Sun Jul 11 2004 - 15:52:45 CDT
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A recent message in this thread(http://amber.ch.ic.ac.uk/archive/200407/0121.html) from David Case
suggested:
./configure -opteron -verbose pgf90
instead of (as tried before)
./configure -opteron -verbose pgf90 -big
Trying this, generated an interesting error:
pgf90 -c -tp k8-32 -O -v -V -Minfo=all -Minform=inform -Mneginfo -o new2oldparm.o _new2oldparm.f
pgf90-Error--tp k8-32 not supported in this installation//usr/pgi/linux86/5.1/bin
I'm using:
[root_at_e01 root]# pgf90 -V
pgf90 5.1-6
I'm assuming the error has occurred because I've only got the 64bit
compiler installed.
Googling (http://mpc.uci.edu/status.html) gave a good explanation of some of the PGI cpu specific flags:
* -tp=k8-32|k8-64|k7|p5|p6|piii|piv|p7|px
* Choose target processor type:
* k8-32 AMD K8 Processor 32-bit mode
* k8-64 AMD K8 Processor 64-bit mode
* k7 AMD Athlon Processor
* p5 Intel Pentium
* p6 Intel P6 Pentium (Pentium Pro, II, III)
* piii Intel Pentium III
* piv Intel Pentium IV
* p7 Intel P7 Pentium IV
* px Intel generic Pentium
Now, why was configure using k8-32? Surely this will only produce 32bit code?
In fact, there is no reference to k8-64 (AMD K8 Processor 64-bit mode) in the configure script:
[root_at_e01 src]# grep "k8-64" configure
[root_at_e01 src]#
No idea why, but replacing every instance of k8-32 with k8-64 in the
config.h (from ./configure -opteron -verbose pgf90) produced a good build!
The majority of the "make test" tests work!, there are some failures in
log.txt.
make clean && make test > log.txt
What follows is quite a verbose listing, my apologies, but I think it's
necessary. The failure is shown along with its relevant dif. I've only
shown the results that did not PASS:
(1)
cd tip5p; ./Run.tip5p
diffing mdout.tip5p.save with mdout
possible FAILURE: check mdout.dif
[root_at_e01 tip5p]# more mdout.dif
191c191
< EKCMT = 0.2952 VIRIAL = 9.6699 VOLUME =
0.0001
--- > EKCMT = 0.2952 VIRIAL = 9.6699 VOLUME = 0.0002(2) cd gb2_trx; ./Run.trxox diffing mdout.trxox.save with mdout.trxox possible FAILURE: check mdout.trxox.dif
[root_at_e01 gb2_trx]# more mdout.trxox.dif 39c39 < gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 --- > gbbeta = 0.00000, gbgamma = 2.90913, surften = 0.00500
(3) cd cnstph; ./Run.cnstph diffing mdout.save with mdout possible FAILURE: check mdout.dif
[root_at_e01 cnstph]# more mdout.dif 45c45 < gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 --- > gbbeta = 0.00000, gbgamma = 2.90913, surften = 0.00500
(4) cd pheTI; ./Run.0; ./Run.1; ./Run.p0; ./Run.p1 diffing out.0.save with out.0 PASSED ============================================================== diffing out.1.save with out.1 PASSED ============================================================== diffing out.p0.save with out.p0 PASSED ============================================================== diffing out.p1.save with out.p1 possible FAILURE: check out.p1.dif
[root_at_e01 pheTI]# more out.p1.dif 190c190 < Ewald error estimate: 0.5094E-16 --- > Ewald error estimate: 0.0000
(5) cd qmmm/standard; ./Run.lysine diffing lysine.out.save with lysine.out possible FAILURE: check lysine.out.dif
[root_at_e01 standard]# more lysine.out.dif 71c71 < 10 -2.1110E-1 9.5830E-1 4.1484 CG 8 --- > 10 -2.1110E-1 9.5830E-1 4.1485 CG 8 83c83 < 20 -6.5331E-1 9.8858E-1 2.8940 N 1 --- > 20 -6.5331E-1 9.8859E-1 2.8941 N 1 91c91 < 20 -6.5331E-1 9.8858E-1 2.8940 N 1 --- > 20 -6.5331E-1 9.8859E-1 2.8941 N 1
(6) cd antechamber/tp; ./Run.tp
diffing tp.prepin.save with tp.prepin PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing prmtop.save with prmtop possible FAILURE: check prmtop.dif
[root_at_e01 tp]# more prmtop.dif 15c15 < -2.15 2.61 -2.07 2.45 -2.49 --- > -2.15 2.60 -2.07 2.45 -2.49 17c17 < 3.00E-1 -4.64 3.48 --- > 2.99E-1 -4.63 3.48
.... diffing prmtop.mol2.save with prmtop.mol2 possible FAILURE: check prmtop.mol2.dif
[root_at_e01 tp]# more prmtop.mol2.dif 15,16c15,16 < -2.15 -2.07 3.00E-1 -2.49 -2.64 < -2.04 2.35 -4.64 3.48 2.45 --- > -2.15 -2.07 2.98E-1 -2.49 -2.64 > -2.04 2.35 -4.63 3.48 2.45
(7) cd antechamber/ash; ./Run.ash
diffing ash.prepin.save with ash.prepin possible FAILURE: check ash.prepin.dif ==============================================================
[root_at_e01 ash]# more ash.prepin.dif 11c11 < 5 HH31 hc E 4 3 2 1. 90. 0. 0.08 --- > 5 HH31 hc E 4 3 2 1. 90. 0. 0.07 15,16c15,16 < 9 O o E 8 4 3 1. 120. 180. -0.61 < 10 N n M 8 4 3 1. 116. 0. -0.57 --- > 9 O o E 8 4 3 1. 120. 180. -0.60 > 10 N n M 8 4 3 1. 116. 0. -0.56 18,20c18,20 < 12 CA c3 M 10 8 4 1. 121. 180. 0.05 < 13 HA h1 E 12 10 8 1. 109. -60. 0.10 < 14 C2 c B 12 10 8 1. 111. -180. 0.64 --- > 12 CA c3 M 10 8 4 1. 121. 180. 0.04 > 13 HA h1 E 12 10 8 1. 109. -60. 0.11 > 14 C2 c B 12 10 8 1. 111. -180. 0.63 26c26 < 20 H2 h1 E 18 16 14 1. 109. 120. 0.04 --- > 20 H2 h1 E 18 16 14 1. 109. 120. 0.03 28,29c28,29 < 22 CB c3 M 12 10 8 1. 111. 60. -0.15 < 23 HB2 hc E 22 12 10 1. 109. -60. 0.11 --- > 22 CB c3 M 12 10 8 1. 111. 60. -0.14 > 23 HB2 hc E 22 12 10 1. 109. -60. 0.10
diffing frcmod.save with frcmod PASSED ============================================================== diffing leap.out.save with leap.out possible FAILURE: check leap.out.dif ==============================================================
[root_at_e01 ash]# more leap.out.dif 1,4c1,4 < -I: Adding dat/leap/prep to search path. < -I: Adding dat/leap/lib to search path. < -I: Adding dat/leap/parm to search path. < -I: Adding dat/leap/cmd to search path. --- > -I: Adding /tmp/amber8.14/dat/leap/prep to search path. > -I: Adding /tmp/amber8.14/dat/leap/lib to search path. > -I: Adding /tmp/amber8.14/dat/leap/parm to search path. > -I: Adding /tmp/amber8.14/dat/leap/cmd to search path. 9,10c9,10 < ----- Source: dat/leap/cmd/leaprc.gaff < ----- Source of dat/leap/cmd/leaprc.gaff done --- > ----- Source: /tmp/amber8.14/dat/leap/cmd/leaprc.gaff > ----- Source of /tmp/amber8.14/dat/leap/cmd/leaprc.gaff done 12c12 < Loading parameters: dat/leap/parm/gaff.dat --- > Loading parameters: /tmp/amber8.14/dat/leap/parm/gaff.dat
diffing prmtop.save with prmtop possible FAILURE: check prmtop.dif
[root_at_e01 ash]# more prmtop.dif 17,19c17,19 < -1.1E+1 -1.0E+1 6.1 9.4E-1 1.8 < 1.1E+1 -1.1E+1 -1.0E+1 6.1 1.4 < 1.3 7.4E-1 4.9E-1 -2.8 2.0 --- > -1.0E+1 -1.0E+1 6.0 7.7E-1 2.0 > 1.1E+1 -1.1E+1 -1.0E+1 6.1 1.3 > 1.3 6.9E-1 5.0E-1 -2.6 1.9
(8) cd antechamber/sustiva; ./Run.sustiva
diffing sustiva.prepin.save with sustiva.prepin possible FAILURE: check sustiva.prepin.dif ==============================================================
[root_at_e01 sustiva]# more sustiva.prepin.dif 11,12c11,12 < 5 C1 ca M 4 3 2 1.3 86.8 -162.9 -0.049 < 6 H1 ha E 5 4 3 1.0 120.1 25.5 0.169 --- > 5 C1 ca M 4 3 2 1.3 86.8 -162.9 -0.047 > 6 H1 ha E 5 4 3 1.0 120.1 25.5 0.168 17c17 < 11 C12 ca M 9 7 5 1.3 119.7 0.1 -0.172 --- > 11 C12 ca M 9 7 5 1.3 119.7 0.1 -0.171 19,24c19,24 < 13 C11 ca M 11 9 7 1.3 119.9 -0.5 0.108 < 14 N1 n M 13 11 9 1.3 121.1 179.9 -0.473 < 15 H7 hn E 14 13 11 0.9 120.1 3.7 0.356 < 16 C10 c M 14 13 11 1.3 124.4 -166.5 0.841 < 17 O2 o E 16 14 13 1.1 123.2 172.5 -0.580 < 18 O1 os M 16 14 13 1.3 115.7 -5.6 -0.376 --- > 13 C11 ca M 11 9 7 1.3 119.9 -0.5 0.106 > 14 N1 n M 13 11 9 1.3 121.1 179.9 -0.471 > 15 H7 hn E 14 13 11 0.9 120.1 3.7 0.355 > 16 C10 c M 14 13 11 1.3 124.4 -166.5 0.838 > 17 O2 o E 16 14 13 1.1 123.2 172.5 -0.579 > 18 O1 os M 16 14 13 1.3 115.7 -5.6 -0.374 26,30c26,30 < 20 C9 c3 3 19 18 16 1.5 105.8 -88.8 0.619 < 21 F1 f E 20 19 18 1.3 110.0 61.2 -0.228 < 22 F2 f E 20 19 18 1.3 110.7 -179.3 -0.230 < 23 F3 f E 20 19 18 1.3 111.5 -58.5 -0.214 < 24 C4 c1 M 19 18 16 1.4 107.2 154.8 -0.197 --- > 20 C9 c3 3 19 18 16 1.5 105.8 -88.8 0.614 > 21 F1 f E 20 19 18 1.3 110.0 61.2 -0.230 > 22 F2 f E 20 19 18 1.3 110.7 -179.3 -0.229 > 23 F3 f E 20 19 18 1.3 111.5 -58.5 -0.215 > 24 C4 c1 M 19 18 16 1.4 107.2 154.8 -0.193 32c32 < 26 C6 cx M 25 24 19 1.4 179.6 -134.9 -0.078 --- > 26 C6 cx M 25 24 19 1.4 179.6 -134.9 -0.079 34c34 < 28 C7 cx M 26 25 24 1.5 119.5 -91.7 -0.107 --- > 28 C7 cx M 26 25 24 1.5 119.5 -91.7 -0.106 36c36 < 30 H4 hc E 28 26 25 1.0 117.3 -0.4 0.082 --- > 30 H4 hc E 28 26 25 1.0 117.3 -0.4 0.083
diffing frcmod.save with frcmod PASSED ============================================================== diffing leap.out.save with leap.out possible FAILURE: check leap.out.dif ==============================================================
[root_at_e01 sustiva]# more leap.out.dif 1,4c1,4 < -I: Adding dat/leap/prep to search path. < -I: Adding dat/leap/lib to search path. < -I: Adding dat/leap/parm to search path. < -I: Adding dat/leap/cmd to search path. --- > -I: Adding /tmp/amber8.14/dat/leap/prep to search path. > -I: Adding /tmp/amber8.14/dat/leap/lib to search path. > -I: Adding /tmp/amber8.14/dat/leap/parm to search path. > -I: Adding /tmp/amber8.14/dat/leap/cmd to search path. 9,10c9,10 < ----- Source: dat/leap/cmd/leaprc.gaff < ----- Source of dat/leap/cmd/leaprc.gaff done --- > ----- Source: /tmp/amber8.14/dat/leap/cmd/leaprc.gaff > ----- Source of /tmp/amber8.14/dat/leap/cmd/leaprc.gaff done 12c12 < Loading parameters: dat/leap/parm/gaff.dat --- > Loading parameters: /tmp/amber8.14/dat/leap/parm/gaff.dat
diffing prmtop.save with prmtop possible FAILURE: check prmtop.dif
[root_at_e01 sustiva]# more prmtop.dif 16,21c16,21 < -3.24 -9.05E-1 3.08 -3.48E-1 -1.36 < -1.21 2.85 -3.14 2.72 1.98 < -8.63 6.49 1.53E+1 -1.05E+1 -6.85 < 5.74 1.12E+1 -4.17 -4.20 -3.91 < -3.59 2.49E-1 -1.43 1.97 -1.95 < 1.46 1.50 -2.04 1.44 1.47 --- > -3.25 -8.58E-1 3.06 -3.54E-1 -1.37 > -1.21 2.85 -3.12 2.72 1.94 > -8.59 6.48 1.52E+1 -1.05E+1 -6.81 > 5.74 1.11E+1 -4.19 -4.18 -3.93 > -3.51 2.53E-1 -1.44 1.97 -1.94 > 1.46 1.51 -2.05 1.45 1.46
(9) cd antechamber/fluorescein; ./Run.fluorescein
Bond types are assigned for valence state 1 with penalty of 2
diffing fluorescein.prepin.save with fluorescein.prepin PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing prmtop.save with prmtop possible FAILURE: check prmtop.dif
[root_at_e01 fluorescein]# more prmtop.dif 17c17 < 2.0 9.1E-3 2.2 -5.7 8.0 --- > 2.0 9.2E-3 2.2 -5.7 8.0
cd antechamber/guanine; ./Run.guanine
diffing DGN.prepin.save with DGN.prepin PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing leap.out.save with leap.out possible FAILURE: check leap.out.dif ==============================================================
[root_at_e01 guanine]# more leap.out.dif 1,4c1,4 < -I: Adding dat/leap/prep to search path. < -I: Adding dat/leap/lib to search path. < -I: Adding dat/leap/parm to search path. < -I: Adding dat/leap/cmd to search path. --- > -I: Adding /tmp/amber8.14/dat/leap/prep to search path. > -I: Adding /tmp/amber8.14/dat/leap/lib to search path. > -I: Adding /tmp/amber8.14/dat/leap/parm to search path. > -I: Adding /tmp/amber8.14/dat/leap/cmd to search path. 9,10c9,10 < ----- Source: dat/leap/cmd/leaprc.gaff < ----- Source of dat/leap/cmd/leaprc.gaff done --- > ----- Source: /tmp/amber8.14/dat/leap/cmd/leaprc.gaff > ----- Source of /tmp/amber8.14/dat/leap/cmd/leaprc.gaff done 12c12 < Loading parameters: dat/leap/parm/gaff.dat --- > Loading parameters: /tmp/amber8.14/dat/leap/parm/gaff.dat
(10) cd pbsa_trx; ./Run.trxox.min diffing mdout.trxox.min.save with mdout.trxox.min possible FAILURE: check mdout.trxox.min.dif
[root_at_e01 pbsa_trx]# more mdout.trxox.min.dif 61c61 < 1 4.6176E+3 2.2342E+1 1.2386E+2 CA 1102 --- > 1 5.8106E+54 2.2342E+1 1.2386E+2 CA 1102 64a65 > EPOLAR = 0.0000 ETHREEB = ************* 68c69 < 1 4.6176E+3 2.2342E+1 1.2386E+2 CA 1102 --- > 1 5.8106E+54 2.2342E+1 1.2386E+2 CA 1102 71a73 > EPOLAR = 0.0000 ETHREEB = *************
(11) cd pbsa_dmp; ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min possible FAILURE: check mdout.dmp.min.dif
[root_at_e01 pbsa_dmp]# more mdout.dmp.min.dif 62c62 < 1 5.9005E+2 2.4154E+2 8.2881E+2 C2 1 --- > 1 5.8106E+54 2.4154E+2 8.2881E+2 C2 1 65a66 > EPOLAR = 0.0000 ETHREEB = ************* 69c70 < 1 5.9005E+2 2.4154E+2 8.2881E+2 C2 1 --- > 1 5.8106E+54 2.4154E+2 8.2881E+2 C2 1 72a74 > EPOLAR = 0.0000 ETHREEB = *************
(12) cd pbsa_ion; ./Run.ion.min diffing mdout.ion.min.save with mdout.ion.min possible FAILURE: check mdout.ion.min.dif
[root_at_e01 pbsa_ion]# more mdout.ion.min.dif 62c62 < 1 -2.0025E+2 0.0000 0.0000 Na+ 1 --- > 1 5.8106E+54 0.0000 0.0000 Na+ 1 65a66 > EPOLAR = 0.0000 ETHREEB = ************* 68c69 < 1 -2.0025E+2 0.0000 0.0000 Na+ 1 --- > 1 5.8106E+54 0.0000 0.0000 Na+ 1 71a73 > EPOLAR = 0.0000 ETHREEB = *************
(13) cd pbsa_pgb; ./Run.pbpgb.min diffing mdout.pbpgb.min.save with mdout.pbpgb.min possible FAILURE: check mdout.pbpgb.min.dif
[root_at_e01 pbsa_pgb]# more mdout.pbpgb.min.dif 61c61 < 1 1.6182E+3 4.2038 2.8914E+1 N 550 --- > 1 5.8106E+54 4.2038 2.8914E+1 N 550 64a65 > EPOLAR = 0.0000 ETHREEB = ************* 68c69 < 1 1.6182E+3 4.2038 2.8914E+1 N 550 --- > 1 5.8106E+54 4.2038 2.8914E+1 N 550 71a73 > EPOLAR = 0.0000 ETHREEB = *************
In summary: The leap.out errors can be ignored; they are due to path differences. The majority of the numerical differences are quite small. The pbsa_* differences are huge!
regards,
Mark Williamson http://dumb.ch.ic.ac.uk/~mjw99/
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- Next message: Ross Walker: "RE: AMBER: MD simulation : problem"
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