AMBER Archive (2006)

Subject: Re: AMBER: installation problem

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon May 15 2006 - 13:25:53 CDT

Lakshmi -
Get the "March 2005 configuration update for pmemd" package from the amber website, amber.scripps.edu. A link to it is at the bottom of the "configuring amber 8 for various architectures section". Once you have gunzip'd and untar'd it, do a "./new_configure -help". NOTE the new_ prefix. I vaguely recollect there is a readme explaining all the hocus-pocus involved. The problem with amber 8 was that it was released right in the teeth of a heck of a lot of compiler and operating system instability, so we basically couldn't get all this stuff right at the time of release.
Best Regards - Bob Duke
  ----- Original Message -----
  From: Mahalakshmi Sahasranaman
  To: amber_at_scripps.edu
  Sent: Monday, May 15, 2006 2:12 PM
  Subject: AMBER: installation problem

  Dear Amber users,

  I have installed Amber8 on pentium 4. I am trying to install pmemd of amber8 on pentium4 and I am having difficulty. I had installed Intel compiler for linux 9.0. SO I did
  source /opt/intel/fc/9.0/bin/ifortvars.sh
  Here below I have attached the contents of my "linux_p4.ifort.nopar" file which I created.
  setenv PREPROCFLAGS "-DDIRFRC_VECT_OPT"

  setenv CPP "/lib/cpp -traditional "

  setenv OPT_LO "ifort -c -auto -tpp7 -mp1 -O0"
  setenv OPT_MED "ifort -c -auto -tpp7 -mp1 -O2"
  setenv OPT_HI "ifort -c -auto -tpp7 -xW -mp1 -ip -O3"

  setenv LOAD "ifort"
  setenv LOADLIB " -limf -lsvml"

  Then I did ./configure linux_p4 ifort nopar and created the config.h file. I did make install in the dir $AMBERHOME/src/pmemd/src and it gets hung up with the following message :

  cd src; make install
  make[1]: Entering directory `/usr/local/amber8/src/pmemd/src'
  ../Compile OPT_HI -P nmr_calls.f90
  cat nmr_calls.f90 | /lib/cpp -traditional -P -DDIRFRC_VECT_OPT > _nmr_calls_.f90
  ifort -c -auto -tpp7 -xW -mp1 -ip -O3 _nmr_calls_.f90
  _nmr_calls_.f90(227) : (col. 2) remark: LOOP WAS VECTORIZED.
  _nmr_calls_.f90(228) : (col. 2) remark: LOOP WAS VECTORIZED.

  Is there any mistake in these ? Please let me know how to get the pmemd of amber8 compiled ?

  Thanks,
  Lakshmi

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