RE: AMBER: Unable to compile amber9

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 24 Jan 2007 07:48:41 -0800

Dear Vinh,
 
I can find no occurance of the string AM_BONDS_broadcast, or any other
AM_*_broadcast for that matter, in the Amber9 source:
 
[07:43][caffeine:0.16][rcw:sander]$ grep AM_BONDS *
amoeba_interface.f: use amoeba_bonds, only : AM_BONDS_readparm
amoeba_interface.f: bonds_valid = AM_BONDS_readparm(nf)
amoeba_interface.f: use amoeba_bonds, only : AM_BONDS_deallocate
amoeba_interface.f: call AM_BONDS_deallocate()
amoeba_interface.f: use amoeba_bonds, only : AM_BONDS_eval
amoeba_interface.f: call AM_BONDS_eval(crd,frc,ene(1),vir_tensor)
amoeba_interface.f: use amoeba_bonds, only : AM_BONDS_set_user_bit
amoeba_interface.f: call AM_BONDS_set_user_bit(do_bond)
...
 
Thus I think you have some modified version of Amber 9. Try the following.
Go back to the original tar file on the cd. Extract this to an empty
directory on your machine. Patch it with bug_fix.all. Then download the
latest g95 compiler from www.g95.org. Numerous bugs in the gfortran compiler
have meant that it always had trouble compiling amber9. This may be fixed in
the latest versions but for the time being I would use g95 which we have
verified to work.
 
Do not make any modifications to the source code.
 
Compile it single processor and then let us know of any errors you see.
 
All the best
Ross

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  _____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Vinh To
Sent: Wednesday, January 24, 2007 06:41
To: amber.scripps.edu
Subject: AMBER: Unable to compile amber9


Hi,

First, this is where I am at:
0) I applied bug_fix_all as of 01-23-2007.
1) Compiling amber9 with gfortran, g95 so far. None of them succeeded.
2) Modified $AMBERHOME/src/arpack/stat.h: "double precision t0, t1, t2, t3,
t4, t5" to "real t0, t1, t2, t3, t4, t5"
3) Replaced some macro/definition with (len=*)

I tried with and without 2) and 3), which got me further but now I
completely stuck at the following (see the end of the email). I compiled
tinker library for amoeba support but the missing symbols dont seem to be in
there.

Let me know if you have further fixing patches. Thank you for the
assistance.

Vinh.

{{{
Starting installation of Amber9 (parallel) at Wed Jan 24 09:37:21 EST 2007.
cd sander; make parallel
make[1]: Entering directory `/nfs/share/vto/tmp/amber9-mod/src/sander'
./checkparconf
cpp -traditional -I/nfs/share/vto/cdi/include -P -DMPI -xassembler-with-cpp
-Dsecond=ambsecond amoeba_interface.f > _amoeba_interface.f
gfortran -c -O3 -fno-second-underscore -march=nocona -ffree-form -o
amoeba_interface.o _amoeba_interface.f
 In file _amoeba_interface.f:133

  use amoeba_bonds, only : AM_BONDS_broadcast
                         1
Error: Symbol 'am_bonds_broadcast' referenced at (1) not found in module
'amoeba_bonds'
 In file _amoeba_interface.f:134

  use amoeba_ureyb, only : AM_UREYB_broadcast
                         1

Error: Symbol 'am_ureyb_broadcast' referenced at (1) not found in module
'amoeba_ureyb'
 In file _amoeba_interface.f:135

  use amoeba_reg_angles, only : AM_REG_ANGLES_broadcast
                              1
Error: Symbol 'am_reg_angles_broadcast' referenced at (1) not found in
module 'amoeba_reg_angles'
 In file _amoeba_interface.f:136

  use amoeba_trig_angles, only : AM_TRIG_ANGLES_broadcast
                               1
Error: Symbol 'am_trig_angles_broadcast' referenced at (1) not found in
module 'amoeba_trig_angles'
 In file _amoeba_interface.f:137

  use amoeba_opbend_angles, only : AM_OPBEND_ANGLES_broadcast
                                 1
Error: Symbol 'am_opbend_angles_broadcast' referenced at (1) not found in
module 'amoeba_opbend_angles'
 In file _amoeba_interface.f:138

  use amoeba_torsions, only : AM_TORSIONS_broadcast
                            1
Error: Symbol 'am_torsions_broadcast' referenced at (1) not found in module
'amoeba_torsions'
 In file _amoeba_interface.f:139

  use amoeba_pitorsions, only : AM_PITORSIONS_broadcast
                              1
Error: Symbol 'am_pitorsions_broadcast' referenced at (1) not found in
module 'amoeba_pitorsions'
 In file _amoeba_interface.f:140

  use amoeba_stretch_bend, only : AM_STRETCH_BEND_broadcast
                                1
Error: Symbol 'am_stretch_bend_broadcast' referenced at (1) not found in
module 'amoeba_stretch_bend'
 In file _amoeba_interface.f:141

  use amoeba_torsion_torsion, only : AM_TOR_TOR_broadcast
                                   1
Error: Symbol 'am_tor_tor_broadcast' referenced at (1) not found in module
'amoeba_torsion_torsion'
 In file _amoeba_interface.f:430

  use amoeba_multipoles, only : AM_MPOLE_broadcast
                              1
Error: Symbol 'am_mpole_broadcast' referenced at (1) not found in module
'amoeba_multipoles'
make[1]: *** [amoeba_interface.o] Error 1
make[1]: Leaving directory `/nfs/share/vto/tmp/amber9-mod/src/sander'
make: *** [parallel] Error 2

}}}





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Received on Sun Jan 28 2007 - 06:07:07 PST
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