AMBER Archive (2006)

Subject: Re: AMBER: pmemd_parallel_ins_prob

From: Amber admin (amber-admin_at_scripps.edu)
Date: Thu Jun 15 2006 - 14:08:46 CDT

Prasenjit -
Okay, this is a pmemd 8 build, so a simple thing to do is look at your
> config.h file for pmemd and modify it such that the values for the
environment variables OPT_MED and OPT_HI are the same as the value for
OPT_LO. You would not want to use this sort of build for much, but you can
at least see if the compiler will not crash if you are not optimizing the
build. If you can't get a compiler update that fixes the problem, and
lowering the optimization works, get back to me and I will tell you how you
can lower the optimization of individual files in the pmemd 8 build process
(I changed the build process for 9, so I have to look this stuff up; let's
make sure it is useful before I bother :-)).
Regards - Bob

----- Original Message -----
From: "pkmukher" <pkmukher_at_olemiss.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, June 08, 2006 2:09 PM
Subject: Re: AMBER: pmemd_parallel_ins_prob

> Robert
>
> Thanks for your advice.I will try to get the latest
> fortran compiler from sgi.Could you also guide me as to how
> i should lower the optimization level of the file.I am a
> novice at these things.Many thanks
>
>
>> Prasenjit,
>> It is a compiler bug, one I have not seen however. Can
>> you get an updated version of the compiler from sgi? If
>> not, you might consider lowering the optimization level
>> for the file that the compiler is processing when it
>> crashes, but I suspect this will not help because the
>> indication is that the compiler cannot parse the file (in
>> other words, it was not generating code when it failed).
>> I would probably also check for repeatability, to insure
>> it is not hardware issues. Regards - Bob Duke
>>
>> ----- Original Message -----
>> From: "pkmukher" <pkmukher_at_olemiss.edu>
>> To: <amber_at_scripps.edu>
>> Sent: Wednesday, June 07, 2006 5:00 PM
>> Subject: AMBER: pmemd_parallel_ins_prob
>>
>>
>> > Hi,
>> >
>> > I am getting the following error message when
>> > installing the pmemd module in the parallel
>> > implementation.It is said that the autoconfiguration
>> > scripst might be causing these problems.If that is the
>> > case could you suggest how i need to modify my
>> > configuration file to get the desired results.The
>> terminal output is given below.I have also added the
>> > output from the hinv command.
>> >
>> > Thanking you in anticipation
>> >
>> >
>> >
>> > uranium 7% ./configure sgi_mips f90 mpi
>> > PMEMD Configurate successfully completed.
>> > uranium 8% make install
>> > cd src; make install
>> > ../Compile OPT_HI -P gbl_constants.f90
>> > cat gbl_constants.f90 | /lib/cpp -P -DMPI
>> > -DDIRFRC_VECT_OPT -DSGIFFT > _gbl_constan
>> > ts_.f90
>> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
>> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
>> > it_intrinsics=ON _gbl_constants_.f90
>> > ../Compile OPT_HI -P gbl_datatypes.f90
>> > cat gbl_datatypes.f90 | /lib/cpp -P -DMPI
>> > -DDIRFRC_VECT_OPT -DSGIFFT > _gbl_datatyp
>> > es_.f90
>> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
>> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
>> > it_intrinsics=ON _gbl_datatypes_.f90
>> > ../Compile OPT_HI -P file_io_dat.f90
>> > cat file_io_dat.f90 | /lib/cpp -P -DMPI
>> > -DDIRFRC_VECT_OPT -DSGIFFT > _file_io_dat_.
>> > f90
>> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
>> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
>> > it_intrinsics=ON _file_io_dat_.f90
>> > touch use_gbl_datatypes.h
>> > ../Compile OPT_HI -P parallel_dat.f90
>> > cat parallel_dat.f90 | /lib/cpp -P -DMPI
>> > -DDIRFRC_VECT_OPT -DSGIFFT > _parallel_dat
>> > _.f90
>> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
>> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
>> > it_intrinsics=ON _parallel_dat_.f90
>> > ../Compile OPT_MED -P file_io.f90
>> > cat file_io.f90 | /lib/cpp -P -DMPI -DDIRFRC_VECT_OPT
>> > -DSGIFFT > _file_io_.f90
>> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
>> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
>> > it_intrinsics=ON _file_io_.f90
>> > touch use_file_io.h
>> > touch use_gbl_constants.h
>> > touch use_parallel_dat.h
>> > ../Compile OPT_HI -P mdin_ctrl_dat.f90
>> > cat mdin_ctrl_dat.f90 | /lib/cpp -P -DMPI
>> > -DDIRFRC_VECT_OPT -DSGIFFT > _mdin_ctrl_dat_.f90
>> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
>> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_bit_intrinsics=ON
>> > _mdin_ctrl_dat_.f90
>> > ../Compile OPT_HI -P axis_optimize_cit.f90
>> > cat axis_optimize_cit.f90 | /lib/cpp -P -DMPI
>> > -DDIRFRC_VECT_OPT -DSGIFFT > _axis_optimize_cit_.f90
>> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
>> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_bit_intrinsics=ON
>> > _axis_optimize_cit_.f90
>> > touch use_axis_optimize_cit.h
>> > touch use_mdin_ctrl_dat.h
>> > ../Compile OPT_HI -P mdin_ewald_dat.f90
>> > cat mdin_ewald_dat.f90 | /lib/cpp -P -DMPI
>> > -DDIRFRC_VECT_OPT -DSGIFFT > _mdin_ewald_dat_.f90
>> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
>> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_bit_intrinsics=ON
>> > _mdin_ewald_dat_.f90
>> > Signal: Bus error in Front End Parse/Semantic phase.
>> > Error: Signal Bus error in phase Front End
>> > Parse/Semantic -- processing aborted
>> > f90 ERROR: /usr/lib32/cmplrs/mfef90 died due to signal
>> > 4 f90 ERROR: core dumped
>> > *** Error code 1 (bu21)
>> > *** Error code 1 (bu21)
>> >
>> > uranium 1% hinv
>> > 8 700 MHZ IP35 Processors
>> > CPU: MIPS R16000 Processor Chip Revision: 2.1
>> > FPU: MIPS R16010 Floating Point Chip Revision: 2.1
>> > Main memory size: 2048 Mbytes
>> > Instruction cache size: 32 Kbytes
>> > Data cache size: 32 Kbytes
>> > Secondary unified instruction/data cache size: 4 Mbytes
>> > Integral SCSI controller 2: Version IDE (ATA/ATAPI) IOC4
>> > Integral SCSI controller 0: Version QL12160, low voltage
>> > differential
>> > Disk drive: unit 1 on SCSI controller 0
>> > Disk drive: unit 2 on SCSI controller 0
>> > Integral SCSI controller 1: Version QL12160, single
>> > ended Disk drive: unit 1 on SCSI controller 1
>> > Disk drive: unit 2 on SCSI controller 1
>> > Disk drive: unit 3 on SCSI controller 1
>> > Disk drive: unit 5 on SCSI controller 1
>> > CDROM: unit 6 on SCSI controller 1
>> > IOC3/IOC4 serial port: tty3
>> > IOC3/IOC4 serial port: tty4
>> > IOC3/IOC4 serial port: tty5
>> > IOC3/IOC4 serial port: tty6
>> > Gigabit Ethernet: tg0, module 001c01, PCI bus 1 slot 4
>> > IOC3/IOC4 external interrupts: 1
>> >
>> >
>> >
>> >
>> > Prasenjit Kumar Mukherjee
>> > Graduate Student
>> > Department of Medicinal Chemistry
>> > School of Pharmacy
>> > University of Mississippi
>> > USA
>> >
>> > Cell - 662 380 0146
>> > Office - 662 915 1286
>> >
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