RE: AMBER: Question about compiling PMEMD

From: Tod Pascal <tpascal.wag.caltech.edu>
Date: Wed, 21 Apr 2004 23:29:55 -0700

Professor Duke,
Thanks for the information. I was able to download version 7.1 and got it
installed. The code seems to compile all the way, however crashes at the
linking stage with the following error:

 

SYSLIB=`../sysdir lib` ; ../Compile LOAD -o pmemd \

                gbl_datatypes.o file_io_dat.o parallel_dat.o mdin_ctrl_dat.o
mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o gbl_dat.o ew_dat.o
ew_direct_cit_dat.o ew_direct_dat.o ew_dipole_dat.o ew_direct_cit.o
ew_recip_cit.o ew_fft_cit.o ew_force_cit.o ew_fft.o ew_bspline.o ew_box.o
force_cit.o runmd_cit.o runmd_cit7.o shake_cit.o runmin_cit.o
axis_optimize_cit.o ew_lib.o pmemd_lib.o runfiles.o file_io.o parallel.o
ew_direct.o ew_recip.o ew_force.o ew_dipole.o ew_recip_dipole.o
ew_recip_reg.o shake.o pmemd_clib.o pmemd.o random.o runmin.o force.o
runmd.o degcnt.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o
alltasks_setup.o ew_setup.o nextprmtop_section.o help.o $SYSLIB;

 

ifc -i_dynamic -o pmemd gbl_datatypes.o file_io_dat.o parallel_dat.o
mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o

inpcrd_dat.o gbl_dat.o ew_dat.o ew_direct_cit_dat.o ew_direct_dat.o
ew_dipole_dat.o ew_direct_cit.o ew_recip_cit.o

ew_fft_cit.o ew_force_cit.o ew_fft.o ew_bspline.o ew_box.o force_cit.o
runmd_cit.o runmd_cit7.o shake_cit.o runmin_cit.o axis_optimize_cit.o
ew_lib.o pmemd_lib.o runfiles.o file_io.o parallel.o ew_direct.o ew_recip.o
ew_force.o ew_dipole.o ew_recip_dipole.o ew_recip_reg.o shake.o pmemd_clib.o
pmemd.o random.o runmin.o force.o runmd.o degcnt.o

nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o alltasks_setup.o
ew_setup.o nextprmtop_section.o help.o ../Machines/intel/sys.a -limf -lsvml
-lPEPCF90 -L/opt/mpich-1.2.4/lib -lpthread -lmpich

parallel_dat.o: In function
`parallel_dat_module..wrapped_cit_mpi_gathervec_.':

parallel_dat.o(.text+0x1e2): undefined reference to `mpi_gatherv_'

parallel_dat.o: In function
`parallel_dat_module..wrapped_cit_mpi_allgathervec_.':

parallel_dat.o(.text+0x5f1): undefined reference to `mpi_allgatherv_'

mdin_ctrl_dat.o: In function `mdin_ctrl_dat_module..bcast_mdin_ctrl_dat_':

mdin_ctrl_dat.o(.text+0x41): undefined reference to `mpi_bcast_'

mdin_ctrl_dat.o(.text+0x84): undefined reference to `mpi_bcast_'

mdin_ewald_dat.o: In function
`mdin_ewald_dat_module..bcast_mdin_ewald_dat_':

mdin_ewald_dat.o(.text+0x41): undefined reference to `mpi_bcast_'

mdin_ewald_dat.o(.text+0x84): undefined reference to `mpi_bcast_'

 

And so on. I think that I might be missing a library, but haven't been able
to figure out what's wrong. Any ideas?

 

Regards,

Tod

 

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

 

  _____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Robert Duke
Sent: Wednesday, April 21, 2004 5:27 AM
To: amber.scripps.edu
Subject: Re: AMBER: Question about compiling PMEMD

 

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 https://premier.intel.com 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 <mailto:tpascal.wag.caltech.edu> Pascal

To: amber.scripps.edu

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

 -P -DLinux -DREGNML -DMPI -DNO_MPI_BUFFER_ALIASING -DSLOW_NONBLOCKING_MPI
-D

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.

contains

^

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.

 

Regards,

 

Tod

 

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 Thu Apr 22 2004 - 09:53:00 PDT
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