AMBER Archive (2004)

Subject: AMBER: Installing Amber on IBM AIX cluster

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Sat Jan 31 2004 - 12:50:30 CST

Dear Ambers
  I am trying to compile Amber on a IBM p690 server.
The compilation fails with an error like the one below. Has somebody
experienced this?
The previous error that I described was due to a wrong Machine.tar file.
I managed with that.
Thank you very much,
vlad

        ../Compile L3 -P -DDPREC ene.f
Building on: IBM,7040-681 under AIX
cat ene.f | /lib/cpp -P -DDPREC -Dibm_aix -DISTAR2 -DMASS -DREGNML
-DNMLEQ -DMEM_ALLOC -DEWALD -DCLINK_PLAIN > _ene_.f
xlf90 -qfixed -O3 -qarch=auto -qtune=auto -c _ene_.f
"_ene_.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the
potential to alter the semantics of a program. Please refer to
documentation on the STRICT/NOSTRICT option for more information.
** bond === End of Compilation 1 ===
"_ene_.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the
potential to alter the semantics of a program. Please refer to
documentation on the STRICT/NOSTRICT option for more information.
** angl === End of Compilation 2 ===
"_ene_.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the
potential to alter the semantics of a program. Please refer to
documentation on the STRICT/NOSTRICT option for more information.
** ephi === End of Compilation 3 ===
"_ene_.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the
potential to alter the semantics of a program. Please refer to
documentation on the STRICT/NOSTRICT option for more information.
** capwat === End of Compilation 4 ===
"_ene_.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the
potential to alter the semantics of a program. Please refer to
documentation on the STRICT/NOSTRICT option for more information.
** xconst === End of Compilation 5 ===
"_ene_.f", line 1232.45: 1515-023 (S) Syntax Error: Illegal token " 1 "
is replaced by token " * ".
"_ene_.f", line 1348.47: 1515-022 (S) Syntax Error: Extra token " 1 "
was found. The token is ignored.
"_ene_.f", line 1348.48: 1515-022 (S) Syntax Error: Extra token " ( "
was found. The token is ignored.
"_ene_.f", line 1348.49: 1515-022 (S) Syntax Error: Extra token " * "
was found. The token is ignored.
"_ene_.f", line 1348.50: 1515-022 (S) Syntax Error: Extra token " ) "
was found. The token is ignored.
"_ene_.f", line 1348.51: 1515-022 (S) Syntax Error: Extra token " , "
was found. The token is ignored.
** xtgtmd === End of Compilation 6 ===
"_ene_.f", line 1495.28: 1515-019 (S) Syntax is incorrect.
"_ene_.f", line 1498.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1499.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1500.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1501.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1502.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1507.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1508.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1509.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1510.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1522.1: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1524.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1526.8: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1527.1: 1514-050 (S) Specification statement is out of
order. Statement is ignored.
"_ene_.f", line 1530.5: 1516-044 (S) A conversion from type LOGICAL is
not permitted.
"_ene_.f", line 1547.10: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1549.11: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1550.11: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1551.11: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1552.11: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1553.11: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1554.11: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1555.11: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1614.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1615.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1616.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1617.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1618.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1619.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1620.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1621.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1622.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1634.6: 1516-044 (S) A conversion from type LOGICAL is
not permitted.
"_ene_.f", line 1645.16: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1646.16: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1653.32: 1516-040 (S) Item has not been defined with the
EXTERNAL or INTRINSIC attribute.
"_ene_.f", line 1653.55: 1516-040 (S) Item has not been defined with the
EXTERNAL or INTRINSIC attribute.
"_ene_.f", line 1658.15: 1516-044 (S) A conversion from type LOGICAL is
not permitted.
"_ene_.f", line 1670.14: 1516-026 (S) Non-arrays must not be subscripted.
"_ene_.f", line 1672.20: 1516-026 (S) Non-arrays must not be subscripted.
"_ene_.f", line 1679.28: 1516-026 (S) Non-arrays must not be subscripted.
"_ene_.f", line 1682.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1692.11: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1698.12: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1710.6: 1516-044 (S) A conversion from type LOGICAL is
not permitted.
"_ene_.f", line 1719.13: 1515-025 (S) Only a name of a variable, array
element, or character substring is permitted on the left hand side of an
assignment statement.
"_ene_.f", line 1781.5: 1516-044 (S) A conversion from type LOGICAL is
not permitted.
** rmsfit === End of Compilation 7 ===
** bellyf === End of Compilation 8 ===
1501-511 Compilation failed for file _ene_.f.
make: 1254-004 The error code from the last command is 1.

Stop.
make: 1254-004 The error code from the last command is 2.

Vlad Cojocaru wrote:

> Dear Carlos and all ambers,
> I tried to make all the changes in les.h, rdparm.f but for that I
> had to compile Amber in a different place (on the same p690 IBM
> cluster) for my own usage.
> I did it th way is indicated in the in the installation guide
> 1. copying the patches
> 2. downloading the Machines tar file
>
>3.ln -s -f Machines/Machine.ibm_aix MACHINE
>4. make install
>
>But I get the followin error:
>make: 1254-002 Cannot find a rule to create target ../Machines/mpi/t3d.h from dependencies.
>Stop.
>make: 1254-004 The error code from the last command is 2.
>
>Could somebody tell me something about this?
>Thank you very much
>vlad
>
>
>
>
> Carlos Simmerling wrote:
>
>>no, that doesn't make sense.
>>you can go into rdparm.f and look for
>>the line with MAXLESADJ. maybe you
>>can add another write statement writing the
>>values of MAXLESADJ and nlesadj.
>>This is about line 645 in my amber7.
>>Carlos
>>
>>----- Original Message -----
>>From: "Vlad Cojocaru" <Vlad.Cojocaru_at_mpi-bpc.mpg.de>
>>To: "amber list" <amber_at_scripps.edu>
>>Sent: Saturday, January 31, 2004 5:40 AM
>>Subject: AMBER: sander.LES on IBM SP cluster
>>
>>
>>
>>
>>>Dear Ambers,
>>> I am trying to run LES with PME on an IBM SP cluster. The last
>>>problem that I had was this message:
>>>LES parameters were found
>>> EXCEEDED MAXLESADJ!
>>>
>>>Then I went to the les.h code and I changed the parameter from 100.000
>>>to 1.000.000, but this only on my local machine. Then the sander.LES
>>>program is running properly on my machine. I got this number : 585570
>>>LES atom pairs require adjustment. So I guessed that MAXLESADJ
>>>represents the maximum no. of LES atom pairs that require adjustment.
>>>
>>>The next step was to do the same thing on an the IBM cluster so that I
>>>can run parrallel. I incresed the same MAXLESADJ to 1.000.000 and then I
>>>recompiled ...move the new executables to ${AMBERHOME}/exe dir. and then
>>>run the simulation again.
>>>
>>>But to my surprise I got the same error message: EXCEEDED MAXLESADJ!
>>>
>>>Did somebody ever encounter such a problem? If yes I would appreciate a
>>>small explanation about it.
>>>Thank you very much
>>>vlad
>>>
>>>--
>>>Vlad Cojocaru
>>>Max Planck Institute for Biophysical Chemistry
>>>Department: 060
>>>Am Fassberg 11, 37077 Goettingen, Germany
>>>tel: ++49-551-201.1327
>>>e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
>>>home tel: ++49-551-9963204
>>>
>>>
>>>
>>>
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>>>
>>>
>>>
>>
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>>
>
>--
>Vlad Cojocaru
>Max Planck Institute for Biophysical Chemistry
>Department: 060
>Am Fassberg 11, 37077 Goettingen, Germany
>tel: ++49-551-201.1327
>e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
>home tel: ++49-551-9963204
>
>
> 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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