Sorry to spam again, but looking at a forum I found through a google search
suggests that LD_INCLUDE_PATH doesn't do anything. try following my advice
on defining MPI_INCLUDE in the config.h first.
All the best,
Jason
On Tue, May 11, 2010 at 11:15 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Sorry, I forgot to mention that the "export" commands I described in my
> last email are POSIX-sh syntax (i.e. sh and bash). To use csh, tcsh, etc.
> syntax, use
>
> setenv LD_INCLUDE_PATH
> "/usr/mpi/gcc/mvapich-1.1.0/include\:$LD_INCLUDE_PATH"
>
> All the best,
> Jason
>
>
> On Tue, May 11, 2010 at 11:14 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> Hello,
>>
>> This is strange, since mpif90 makes a soft link to mpif.h in the local
>> directory. This suggests that neither the local directory nor
>> /usr/mpi/gcc/mvapich-1.1.0/include are in the searched include path (I'm
>> guessing LD_INCLUDE_PATH, since the libraries are searched in
>> LD_LIBRARY_PATH).
>>
>> I see two options to fix this (though you may want to talk to your system
>> admin as to why the linker can't find the mpif.h header file in the local
>> directory). #1: use the following command before you begin to compile
>>
>> export
>> LD_INCLUDE_PATH=/usr/mpi/gcc/mvapich-1.1.0/include\:$LD_INCLUDE_PATH
>>
>> Or, #2: change MPI_INCLUDE back to its default value in config.h. namely:
>>
>>
>> MPI_INCLUDE = -I$(MPI_HOME)/include
>>
>> Something worth trying may also be to just add the present directory to
>> LD_INCLUDE_PATH (which may be a good permanent solution considering what
>> mpif90 is trying to do, though more experienced users may have advice
>> against this):
>>
>> export LD_LIBRARY_PATH=.\:$LD_INCLUDE_PATH
>>
>> I think that any of the above 3 solutions should be sufficient to resolve
>> that error (though of course I have no way of knowing if there will be other
>> errors after this one).
>>
>> If this doesn't work, check the directory
>> /usr/mpi/gcc/mvapich-1.1.0/include . Is there a file called mpif.h in
>> there? If not, that is definitely your problem. Considering how easy this
>> check is, that is probably worth doing first. If it exists in that
>> directory, then any of the above should fix it. If it's not, try googling
>> the issue to see what comes up (the MPI may need to be reinstalled?) I just
>> checked mvapich, mvapich2, mpich2, and openmpi installations on machines I
>> have access to, and every single one has mpif.h in the $MPI_HOME/include
>> directories (as I would expect them to), so it should be there.
>>
>> Good luck!
>> Jason
>>
>>
>> On Tue, May 11, 2010 at 9:38 PM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
>>
>>> Thanks Jason. I compiled Amber10 just few months back and applied all
>>> bugfixes that time. (I tried again today and it skipped all patches).
>>> ***********************************
>>> # mpif90 -show
>>> ln -s /usr/mpi/gcc/mvapich-1.1.0/include/mpif.h mpif.h
>>> gfortran -fPIC -fPIC -L/usr/lib64 -Wall -Wl,-rpath-link
>>> -Wl,/usr/mpi/gcc/mvapich-1.1.0/lib/shared
>>> -L/usr/mpi/gcc/mvapich-1.1.0/lib/shared -L/usr/mpi/gcc/mvapich-1.1.0/lib
>>> -lmpichf90nc -lmpichfarg -lmpich -L/usr/lib64 -libverbs -libumad -libcommon
>>> -lpthread -Wall -lpthread -lrt
>>> rm -f mpif.h
>>> ************************************
>>> so it is picking up the right compiler. Good news is that we narrowed
>>> down to just one error now.
>>> **************************************
>>> [tripos.craycx1 pmemd]$ make install
>>> cd src && make install
>>> make[1]: Entering directory
>>> `/home/tripos/amber10_install/amber10/src/pmemd/src'
>>> /lib/cpp -traditional -P -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS
>>> -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC gbl_constants.fpp gbl_constants.f90
>>> mpif90 -c -O3 gbl_constants.f90
>>> /lib/cpp -traditional -P -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS
>>> -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC gbl_datatypes.fpp gbl_datatypes.f90
>>> mpif90 -c -O3 gbl_datatypes.f90
>>> /lib/cpp -traditional -P -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS
>>> -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC state_info.fpp state_info.f90
>>> mpif90 -c -O3 state_info.f90
>>> /lib/cpp -traditional -P -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS
>>> -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC file_io_dat.fpp file_io_dat.f90
>>> mpif90 -c -O3 file_io_dat.f90
>>> /lib/cpp -traditional -P -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS
>>> -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC pmemd_lib.fpp pmemd_lib.f90
>>> pmemd_lib.fpp:40: error: mpif.h: No such file or directory
>>> make[1]: *** [pmemd_lib.o] Error 1
>>> make[1]: Leaving directory
>>> `/home/tripos/amber10_install/amber10/src/pmemd/src'
>>> make: *** [install] Error 2
>>> **************************************************
>>>
>>> $MPI_HOME/bin is very much in the path(please see the out put for
>>> mpif90 -show above).
>>> any suggestions?
>>>
>>> thanks in advance..
>>>
>>> Senthil
>>>
>>>
>>>
>>>
>>>
>>>
>>> Hello,
>>>
>>> First thing to always check:
>>>
>>> all bugfixes have been downloaded and applied. Then try recompiling (but
>>> make clean before every fresh try!). If these don't work, see my advice
>>> below:
>>>
>>> I would probably opt for using the compiler wrappers (as long as you know
>>> they've been properly installed with your MPI). Doing this, you can get
>>> rid
>>> of everything in front of MPI_INCLUDE and MPI_LIBS (since mpif90 will
>>> take
>>> care of that for you).
>>>
>>> Then, change F90 = gfortran to F90 = mpif90 and LOAD = gfortran to LOAD =
>>> mpif90 . See the comments below for clarification:
>>>
>>> On Tue, May 11, 2010 at 6:13 PM, Senthil Natesan <sen.natesan.yahoo.com
>>> >wrote:
>>>
>>> > Dear Amber Users,
>>> >
>>> > I am installing PMEMD (Amber 10) on RHEL 5.3 (x86_64) using gfortran
>>> and
>>> > mvapichand got some errors. I am displaying my config.h file here and
>>> > please see the attachment for error output.
>>> >
>>> > config.h:
>>> > -----------------------------
>>> > MATH_DEFINES =
>>> > MATH_LIBS =
>>> > FFT_DEFINES = -DPUBFFT
>>> > FFT_INCLUDE =
>>> > FFT_LIBS =
>>> > NETCDF_HOME =
>>> > NETCDF_DEFINES =
>>> > NETCDF_MOD =
>>> > NETCDF_LIBS =
>>> > MPI_HOME = /usr/mpi/gcc/mvapich-1.1.0
>>> > MPI_LIBDIR2 = /usr/mpi/gcc/mvapich-1.1.0/lib/shared
>>> > MPI_DEFINES = -DMPI
>>> > MPI_INCLUDE = -I$(MPI_HOME)/include
>>> >
>>>
>>> change to
>>>
>>> MPI_INCLUDE =
>>>
>>>
>>> > MPI_LIBDIR = $(MPI_HOME)/lib
>>> > MPI_LIBS = -L$(MPI_LIBDIR) -lmpich -L$(MPI_LIBDIR2) -lmtl_common -lvapi
>>> > -lmosal -lmpga -lpthread
>>> >
>>>
>>> change to
>>>
>>> MPI_LIBS =
>>>
>>>
>>> > DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
>>> > CPP = /lib/cpp
>>> > CPPFLAGS = -traditional -P
>>> > F90_DEFINES = -DFFTLOADBAL_2PROC
>>> >
>>> > F90 = gfortran
>>> >
>>>
>>> change to
>>>
>>> F90 = mpif90
>>>
>>>
>>> > MODULE_SUFFIX = mod
>>> > F90FLAGS = -c
>>> > F90_OPT_DBG = -g -ftrace=full
>>> > F90_OPT_LO = -O0
>>> > F90_OPT_MED = -O2
>>> > F90_OPT_HI = -O3
>>> > F90_OPT_DFLT = $(F90_OPT_HI)
>>> > CC = gcc
>>> > CFLAGS =
>>> >
>>> > LOAD = gfortran
>>> >
>>>
>>> change to
>>>
>>> LOAD = mpif90
>>>
>>>
>>> > LOADFLAGS =
>>> > LOADLIBS =
>>> > -------------------------------------------------
>>> >
>>> > Any suggestions would be very helpful. Thanks,
>>> >
>>> > Senthil Natesan
>>> >
>>>
>>> However, a simple check to make sure that mpif90 is invoking the correct
>>> compiler is:
>>>
>>> mpif90 -show
>>>
>>> This should show you the include directories and library directories that
>>> it's providing as well as the specific libraries it's using.
>>>
>>> Hope this helps,
>>> Jason
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Graduate Student
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 11 2010 - 20:30:06 PDT
