AMBER Archive (2008)

Subject: Re: AMBER: the pmemd problem

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Jul 25 2008 - 08:46:24 CDT

Well, openmpi is not lam. Install lam, or look on the amber reflector list about the various hacked-up attempts to support openmpi. I did not support openmpi in pmemd 9 because 1) it came out about the time of the release and had rather minimal documentation, 2) mpich 1 and 2 and lam had the same functionality and were both well documented and tested, and 3) due to constraints on my time. I think Ross has since put stuff on the reflector about using openmpi (in reality, if you actually read the README shipped with pmemd, it tells you how to adopt a new mpi implementation). I am not jumping up and down to get support for openmpi "out there" because I have had reports that at least compared to mvapich on infiniband, the performance is pretty bad, and in general, I don't list something as "supported" unless I have actually been able to thoroughly test it. So what about the actual errors below? The "-tp not supported" stuff is version 10 compiler whining over options to select processor type that is relatively harmless I believe. PMEMD 9 shipped in the timeframe that ifort 8 was available, not 10 (it could be the earliest releases of 9 were also there). This sort of thing is a continual problem with changes in compilers, math libraries, fft libraries, etc. We need to track it better, sense the compiler versions, etc. It would be nice if intel had a little sense about backward compatibility in software; it won the chip wars largely by realizing the importance of backward compatibility in hardware. Anybody up to make a career out of configuration? The "Cannot open include file 'mpif-common.h'" message occurs because the main mpi header file, which is found by pmemd, then references include files in some other subdirectory, which was not configured to be part of the MPI_INCLUDE script variable. I would think you can probably get a lot of this stuff right by seeing what you get from entering "mpif77 -link_info" (or see what sander uses in the outer configure.h; there has been a bigger effort to get auto-configuration running for sander and the rest of amber, but that part of amber does not routinely have to hit all the supercomputer configurations that pmemd also is configured for). This may NOT be the correct command for openmpi - I don't have it installed anywhere, but it works for mpich 1 and 2, and I think it was sort of a followon effort.
Regards - Bob Duke

----- Original Message -----
  From: hklwatergod
  To: amber
  Sent: Friday, July 25, 2008 7:51 AM
  Subject: AMBER: the pmemd problem

  Dear all:

  whem i installed pmemd 9.0 ,i got the following errors. i used the openmpi 1.2.6 and ifort
  ./configure linux_p4 ifort lam pubfft nobintraj

  Intel ifort compiler found; version information:
  Version 10.1
  Use Intel MKL? (better performance) (answer yes or no):
  no
  File config_data/fft.pubfft being used...
  File config_data/linux_p4.ifort being used...
  File config_data/interconnect.lam being used...
  configure assumes lam files are in /opt/openmpi.
  PMEMD Configurate successfully completed.

  make install
  make[1]: Entering directory `/usr/local/amber9/src/pmemd/src'
  /lib/cpp -traditional -P -I/opt/openmpi/include -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_COMTRANS -DDIRFRC_EFS -DFFTLOADBAL_2PROC gbl_constants.fpp gbl_constants.f90
  ifort -c -auto -tpp7 -xN -ip -O3 gbl_constants.f90
  ifort: command line remark #10148: option '-tp' not supported
  /lib/cpp -traditional -P -I/opt/openmpi/include -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_COMTRANS -DDIRFRC_EFS -DFFTLOADBAL_2PROC gbl_datatypes.fpp gbl_datatypes.f90
  ifort -c -auto -tpp7 -xN -ip -O3 gbl_datatypes.f90
  ifort: command line remark #10148: option '-tp' not supported
  /lib/cpp -traditional -P -I/opt/openmpi/include -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_COMTRANS -DDIRFRC_EFS -DFFTLOADBAL_2PROC state_info.fpp state_info.f90
  ifort -c -auto -tpp7 -xN -ip -O3 state_info.f90
  ifort: command line remark #10148: option '-tp' not supported
  /lib/cpp -traditional -P -I/opt/openmpi/include -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_COMTRANS -DDIRFRC_EFS -DFFTLOADBAL_2PROC file_io_dat.fpp file_io_dat.f90
  ifort -c -auto -tpp7 -xN -ip -O3 file_io_dat.f90
  ifort: command line remark #10148: option '-tp' not supported
  /lib/cpp -traditional -P -I/opt/openmpi/include -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_COMTRANS -DDIRFRC_EFS -DFFTLOADBAL_2PROC parallel_dat.fpp parallel_dat.f90
  ifort -c -auto -tpp7 -xN -ip -O3 parallel_dat.f90
  ifort: command line remark #10148: option '-tp' not supported
  fortcom: Error: parallel_dat.f90, line 92: Cannot open include file 'mpif-common.h'
        include 'mpif-common.h'
  --------------^
  fortcom: Error: parallel_dat.f90, line 224: This name does not have a type, and must have an explicit type. [MPI_COMM_WORLD]
      call mpi_abort(mpi_comm_world, i, err_ret_code)
  -------------------^
  compilation aborted for parallel_dat.f90 (code 1)
  make[1]: *** [parallel_dat.o] Error 1
  make[1]: Leaving directory `/usr/local/amber9/src/pmemd/src'

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  hklwatergod
  2008-07-25

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