Re: AMBER: Question about compiling PMEMD

From: Robert Duke <>
Date: Wed, 21 Apr 2004 08:27:02 -0400

Tod -
There is no workaround. Period. I tried. The 8.0 compiler is really messed up for some inputs (my guess would be f90 code that makes use of lots of modules, which is what distinguishes pmemd from the rest of amber). So you should have gotten a chance to set up some sort of semi-support account when you got ifort (or full support if you bought it). Using that account go to website, log in, and get through the confidentiality page, ending up on your account page. Ignore the "what's new" page(s) of downloads that comes up (you want something old). To the left, under premier features, click on "file downloads". Look down the filelist to stuff released 1/8/2004. Click on l_fc_pc_7.1.038.tar and download it. Don't lose it, in case they remove it from the site before they fix its successors. The status on the intel compilers is that 8.0 is broken in regards to pmemd, and may not be fixed until they release 8.1, and 7.1.038 is the last working version of 7.1 with regards to pmemd (they broke the later releases, and don't consider the fixes critical, since there is a workaround). Regarding intel compilers, I would grab versions that work and not get rid of them until I am certain the next thing is okay. Intel seems to have recently lost the ability to actually achieve a net reduction in their compiler defects. They also have superceded working versions of the itanium ifort 8.0 compilers with broken ones, so you have to watch out there. Note that for the itanium, though, the 8.0 compilers in general DO work. The bulk of the problems seem to be arising in grafting the compaq compiler frontend on top of their IA32 backend, which is what happened in 8.0. They did the same thing for the itanium, but seem to have not had as much trouble there.
Regards - Bob Duke
  ----- Original Message -----
  From: Tod Pascal
  Sent: Wednesday, April 21, 2004 3:21 AM
  Subject: AMBER: Question about compiling PMEMD

  Hello All,

  I'm trying to install PMEMD on a P4 Red Hat 8 cluster (with MPI) using the IFC 8.0. I'm aware that there is a bug that prevents the installation, however I was hoping there was a work-around, since the version of IFC I've gotten from Intel is version 8 (and I'm unaware how to obtain version 7.1). The installation crashes with the following error:


  ../Compile L3 -P ew_direct_cit_dat.f90

  cat ew_direct_cit_dat.f90 | /lib/cpp -traditional -I/opt/mpich-1.2.4//include


  SHORT=INTEGER(2) -DLOGICAL_BYTE=LOGICAL(1) > _ew_direct_cit_dat_.f90

  ifc -c -auto -tpp6 -mp1 -ip -O3 _ew_direct_cit_dat_.f90

  ifc: warning: The Intel Fortran driver is now named ifort. You can suppress th

  is message with '-quiet'

  fortcom: Severe: _ew_direct_cit_dat_.f90, line 81: **Internal compiler error: s

  egmentation violation signal raised** Please report this error along with the c

  ircumstances in which it occurred in a Software Problem Report. Note: File and

   line given may not be explicit cause of this error.



  compilation aborted for _ew_direct_cit_dat_.f90 (code 3)

  make[1]: *** [ew_direct_cit_dat.o] Error 1

  make[1]: Leaving directory `/net/hulk/home3/tpascal/amber7/src.pmemd/pmemd'



  Is this error familiar, and if so do you have any suggestions? I've tried compiling this file with a lower level of optimization (from L0 - L3) to no avail.






  The glass is neither half empty nor half full. It was simply designed too large to begin with.
  -- Some Engineer


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Received on Wed Apr 21 2004 - 13:53:01 PDT
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