RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler from Mark Williamson on 2004-07-11 (Amber Archive Jul 2004)

From: Mark Williamson <mark.williamson.imperial.ac.uk>
Date: Sun, 11 Jul 2004 21:52:45 +0100

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.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.e01 src]# grep "k8-64" configure
[root.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Sun Jul 11 2004 - 22:53:00 PDT