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-- Thanks Best rgds Amit D M Systems Pvt. Ltd. B-127, Shivalik, ND – 17 Ph – 26691429/2344 98112-07764 “One never reaches anywhere sitting on the shore” -----Original Message----- From: "Ross Walker" <ross.rosswalker.co.uk> To: <amber.scripps.edu> Date: Mon, 22 Dec 2008 09:46:58 -0800 Subject: RE: AMBER: amber 9 compilation error with mvapich and intel compilers Hi Amit, I would recommend doing the following. Firstly make sure that the version of mvapich you are linking to was built with the same compiler as you are using to build AMBER. For example the following comes from Ranger (http://www.tacc.utexas.edu/resources/hpcsystems/) and highlights how I compiled amber9 with mvapich on it: login3% which mpif90 /opt/apps/pgi7_2/mvapich/1.0.1/bin/mpif90 The path here implies that PGI v7.2 was used to build this version of MVAPICH. If your system admin is any good they should have built several versions of mvapich for each different compiler option on your machine. We can further check what compiler is being used by asking the mpif90 script what it is actually doing: login3% mpif90 -show ln -s /opt/apps/pgi7_2/mvapich/1.0.1/include/mpif.h mpif.h pgf90 -Wl,-rpath,/opt/apps/pgi7_2/mvapich/1.0.1/lib/shared -Wl,-rpath-link -Wl,/opt/apps/pgi7_2/mvapich/1.0.1/lib/shared -L/opt/apps/pgi7_2/mvapich/1.0.1/lib/shared -L/opt/apps/pgi7_2/mvapich/1.0.1/lib -lmpichf90nc -lmpichfarg -lmpich -L/opt/ofed//lib64/ -libverbs -libumad -lpthread -lpthread -lrt Here we see if runs pgf90. We can then check that the pgf90 in our path is the same version as was used for mvapich: login3% which pgf90 /opt/apps/pgi/7.2-5/linux86-64/7.2-5/bin/pgf90 All looks good. Next we can configure amber9: setenv AMBERHOME ~/amber9 tar xvzf amber9.tgz cd amber9 wget http://ambermd.org/bugfixes/9.0/bugfix.all patch -p0 -N -r patch_rejects < bugfix.all cd src ./configure -mpi pgf90 Edit config.h and change all occurrences of pgf90 to mpif90. Also remove all occurrences of -lmpi. On the end of the FPPFLAGS line add: -I/opt/apps/pgi7_2/mvapich/1.0.1/include/ Since 64 bit pgi compilations used to fail with the version of PGI available at AMBER 9 release it also forced 32 bit compilation which with v7.2 we can now allow - so also remove -tp p7 and -m32. (Just be sure to run all the test cases and make sure they work.) - other compilers such as ifort do not have this issue. make parallel This should compile properly - then you can go on and run the parallel tests as normal. All the best Ross From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of Amit Bajaj Sent: Sunday, December 21, 2008 9:42 PM To: amber.scripps.edu Subject: Re: AMBER: amber 9 compilation error with mvapich and intel compilers dear david we used mvapich 1.x so we provided option "mpich" while generating config.h Thanks Best rgds Amit D M Systems Pvt. Ltd. B-127, Shivalik, ND – 17 Ph – 26691429/2344 98112-07764 “One never reaches anywhere sitting on the shore” David A. Case wrote: On Sat, Dec 20, 2008, Amit Bajaj wrote: We are trying to compile Amber 9 (sander) with mvapich(we got it as part of mellanox OpenFabrics Enterprise Distribution for Linux on RHEL 4(64 bit) on Intel 5400 series processor How did you configure the system? Amber 9's configure script does not offer any option for mvapich, so I'm assuming you must have done some editing of config.h (or something) on your own. /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(viapriv.o)(.text+0x155): In function `viadev_ext_sendq_send': : undefined reference to `prepare_coalesced_pkt' Note that these are undefined references coming from the mpi library, which suggests that you are not linking in the correct libraries. Be sure you can compile and run the test cases (or other simple MPI programs) that come with you mpi installation. ...dac ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.edu ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.edu ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.eduReceived on Wed Dec 24 2008 - 01:12:24 PST