[mpich-discuss] linking MPI
Gus Correa
gus at ldeo.columbia.edu
Mon Oct 24 16:19:45 CDT 2011
Hi Carolina
The compiler wrapper is called mpif90, not mpichf90,
this is why 'which' cannot find it.
If you change FC to /full/path/to/mpich2/bin/mpif90 in your
makefile, it should be easier to compile.
I hope this helps,
Gus Correa
Carolina Carneiro wrote:
> Hi guys,
>
> I think the path to install directory was wrong, what's strange since I
> did exactly what the mpich's read me said. Now I got this error:
>
> root at carol-HP-Pavilion-dv5-Notebook-PC:/home/carol/mocassin/mocassin.2.02.69#
> make mocassin
> /home/carol/mocassin/mpich2-1.4.1p1/bin/mpif90 -O5 -o mocassin
> source/infnan.f90 source/constants_mod.f90 source/vector_mod.f90
> source/common_mod.f90 source/interpolation_mod.f90
> source/set_input_mod.f90 source/hydro_mod.f90 source/ph_mod.f90
> source/composition_mod.f90 source/continuum_mod.f90
> source/ionization_mod.f90 source/pathIntegration_mod.f90
> source/grid_mod.f90 source/dust_mod.f90 source/emission_mod.f90
> source/photon_mod.f90 source/update_mod.f90 source/output_mod.f90
> source/iteration_mod.f90 source/mocassin.f90
> -l/home/carol/mocassin/mpich2-1.4.1p1/src/include
> source/common_mod.f90(240): warning #6379: The structure contains one or
> more misaligned fields. [GRID_TYPE]
> type grid_type ! derived grid type
> ---------^
> source/emission_mod.f90(3109): remark #8291: Recommended relationship
> between field width 'W' and the number of fractional digits 'D' in this
> edit descriptor is 'W>=D+7'.
>
> read(unit=19,fmt='(A2,I2,1x,A23,11x,A7,1x,F9.4,7x,F9.6,4x,F12.6,1x,I2,1x,I2,1x,E8.2,1x,E8.2,1x,I2)',
> &
> -----------------------------------------------------------------------------------------^
> source/emission_mod.f90(3109): remark #8291: Recommended relationship
> between field width 'W' and the number of fractional digits 'D' in this
> edit descriptor is 'W>=D+7'.
>
> read(unit=19,fmt='(A2,I2,1x,A23,11x,A7,1x,F9.4,7x,F9.6,4x,F12.6,1x,I2,1x,I2,1x,E8.2,1x,E8.2,1x,I2)',
> &
> -------------------------------------------------------------------------------------------------^
> source/iteration_mod.f90(544): warning #8093: A do-variable within a DO
> body shall not appear in a variable definition context. [GPLOC]
> & gpLoc=gpLoc, cellLoc=cellLoc)
> ---------------------------------------------^
> source/iteration_mod.f90(547): warning #8093: A do-variable within a DO
> body shall not appear in a variable definition context. [GPLOC]
> & gpLoc=gpLoc, cellLoc=cellLoc)
> ---------------------------------------------^
> ld: cannot find
> -lroot at carol-HP-Pavilion-dv5-Notebook-PC:/home/carol/mocassin/mocassin.2.02.69#
> make mocassin
> /home/carol/mocassin/mpich2-1.4.1p1/bin/mpif90 -O5 -o mocassin
> source/infnan.f90 source/constants_mod.f90 source/vector_mod.f90
> source/common_mod.f90 source/interpolation_mod.f90
> source/set_input_mod.f90 source/hydro_mod.f90 source/ph_mod.f90
> source/composition_mod.f90 source/continuum_mod.f90
> source/ionization_mod.f90 source/pathIntegration_mod.f90
> source/grid_mod.f90 source/dust_mod.f90 source/emission_mod.f90
> source/photon_mod.f90 source/update_mod.f90 source/output_mod.f90
> source/iteration_mod.f90 source/mocassin.f90
> -l/home/carol/mocassin/mpich2-1.4.1p1/src/include
> source/common_mod.f90(240): warning #6379: The structure contains one or
> more misaligned fields. [GRID_TYPE]
> type grid_type ! derived grid type
> ---------^
> source/emission_mod.f90(3109): remark #8291: Recommended relationship
> between field width 'W' and the number of fractional digits 'D' in this
> edit descriptor is 'W>=D+7'.
>
> read(unit=19,fmt='(A2,I2,1x,A23,11x,A7,1x,F9.4,7x,F9.6,4x,F12.6,1x,I2,1x,I2,1x,E8.2,1x,E8.2,1x,I2)',
> &
> -----------------------------------------------------------------------------------------^
> source/emission_mod.f90(3109): remark #8291: Recommended relationship
> between field width 'W' and the number of fractional digits 'D' in this
> edit descriptor is 'W>=D+7'.
>
> read(unit=19,fmt='(A2,I2,1x,A23,11x,A7,1x,F9.4,7x,F9.6,4x,F12.6,1x,I2,1x,I2,1x,E8.2,1x,E8.2,1x,I2)',
> &
> -------------------------------------------------------------------------------------------------^
> source/iteration_mod.f90(544): warning #8093: A do-variable within a DO
> body shall not appear in a variable definition context. [GPLOC]
> & gpLoc=gpLoc, cellLoc=cellLoc)
> ---------------------------------------------^
> source/iteration_mod.f90(547): warning #8093: A do-variable within a DO
> body shall not appear in a variable definition context. [GPLOC]
> & gpLoc=gpLoc, cellLoc=cellLoc)
> ---------------------------------------------^
> ld: cannot find -l/home/carol/mocassin/mpich2-1.4.1p1/src/include
> ld: cannot find -lmpichf90
> ld: cannot find -lmpichf90
> make: *** [mocassin] Error 1
>
>
> the directory path /home/carol/mocassin/mpich2-1.4.1p1/src/include is
> right, but this file mpichf90 I can't find. When I try "locate mpichf90"
> nothing happens.
>
> Carolina.
>
> 2011/10/24 Gus Correa <gus at ldeo.columbia.edu <mailto:gus at ldeo.columbia.edu>>
>
> HI Carolina
>
> It is easier to use the MPI compiler wrapper than the
> bare compiler, because the wrapper knows the MPI libraries it needs,
> the MPI include files it needs, and where to find them.
>
> I.e. try to change the F90 macro in the makefile to
> F90=/your/path/to/mpich2/bin/__mpif90
>
>
> My two cents,
> Gus Correa
>
>
> Carolina Carneiro wrote:
>
> Hi,
>
> I'm having problems to use the command make to compile a
> makefile. I'm trying to link the makefile to the MPI library,
> but it isn't working. Several errors are appearing:
>
> root at carol-HP-Pavilion-dv5-__Notebook-PC:/home/carol/__mocassin/mocassin.2.02.69#
> make mocassin
> /opt/intel/composer_xe_2011___sp1.6.233/composer_xe_2011___sp1.6.233/bin/intel64/ifort
> -O5 -o mocassin source/infnan.f90 source/constants_mod.f90
> source/vector_mod.f90 source/common_mod.f90
> source/interpolation_mod.f90 source/set_input_mod.f90
> source/hydro_mod.f90 source/ph_mod.f90
> source/composition_mod.f90 source/continuum_mod.f90
> source/ionization_mod.f90 source/pathIntegration_mod.f90
> source/grid_mod.f90 source/dust_mod.f90 source/emission_mod.f90
> source/photon_mod.f90 source/update_mod.f90
> source/output_mod.f90 source/iteration_mod.f90
> source/mocassin.f90 -l/home/carol/mocassin/__mpich2install/include
> source/common_mod.f90(240): warning #6379: The structure
> contains one or more misaligned fields. [GRID_TYPE]
> type grid_type ! derived grid type
> ---------^
> source/grid_mod.f90(491): error #5102: Cannot open include file
> 'mpif.h'
> include 'mpif.h'
> ----------------^
> compilation aborted for source/grid_mod.f90 (code 1)
> source/dust_mod.f90(17): error #5102: Cannot open include file
> 'mpif.h'
> include 'mpif.h'
> --------------^
> source/dust_mod.f90(97): error #6404: This name does not have a
> type, and must have an explicit type. [MPI_REAL]
> & mpi_real, mpi_sum, mpi_comm_world,
> ierr)
> ------------------------------__^
> source/dust_mod.f90(97): error #6404: This name does not have a
> type, and must have an explicit type. [MPI_SUM]
> & mpi_real, mpi_sum, mpi_comm_world,
> ierr)
> ------------------------------__----------^
> source/dust_mod.f90(97): error #6404: This name does not have a
> type, and must have an explicit type. [MPI_COMM_WORLD]
> & mpi_real, mpi_sum, mpi_comm_world,
> ierr)
> ------------------------------__-------------------^
> compilation aborted for source/dust_mod.f90 (code 1)
> source/emission_mod.f90(8): error #7013: This module file was
> not generated by any release of this compiler. [GRID_MOD]
> use grid_mod
> --------^
> source/emission_mod.f90(217): error #6404: This name does not
> have a type, and must have an explicit type. [GETVOLUME]
> dV = getVolume(grid,ix,iy,iz)
> -------------^
> source/emission_mod.f90(536): error #6404: This name does not
> have a type, and must have an explicit type. [HLEVXSECP]
> phXSecHI = xSecArray(i-HIPnuP+1+__HlevXSecP(1)-1)
> ------------------------------__---------------^
> source/emission_mod.f90(545): error #6404: This name does not
> have a type, and must have an explicit type. [HEISINGXSECP]
> phXSecHeI =
> xSecArray(i-HeIPnuP+1+__HeISingXSecP(1)-1)
> ------------------------------__--------------------^
> source/emission_mod.f90(553): error #6404: This name does not
> have a type, and must have an explicit type. [HEIIXSECP]
> phXSecHeII =
> xSecArray(i-HeIIPnuP+1+__HeIIXSecP(1)-1)
> ------------------------------__--------------------------^
> source/emission_mod.f90(3109): remark #8291: Recommended
> relationship between field width 'W' and the number of
> fractional digits 'D' in this edit descriptor is 'W>=D+7'.
>
> read(unit=19,fmt='(A2,I2,1x,__A23,11x,A7,1x,F9.4,7x,F9.6,4x,__F12.6,1x,I2,1x,I2,1x,E8.2,1x,__E8.2,1x,I2)',
> &
> ------------------------------__------------------------------__-----------------------------^
> source/emission_mod.f90(3109): remark #8291: Recommended
> relationship between field width 'W' and the number of
> fractional digits 'D' in this edit descriptor is 'W>=D+7'.
>
> read(unit=19,fmt='(A2,I2,1x,__A23,11x,A7,1x,F9.4,7x,F9.6,4x,__F12.6,1x,I2,1x,I2,1x,E8.2,1x,__E8.2,1x,I2)',
> &
> ------------------------------__------------------------------__------------------------------__-------^
> compilation aborted for source/emission_mod.f90 (code 1)
> source/photon_mod.f90(9): error #7013: This module file was not
> generated by any release of this compiler. [GRID_MOD]
> use grid_mod
> --------^
> compilation aborted for source/photon_mod.f90 (code 1)
> source/update_mod.f90(8): error #7013: This module file was not
> generated by any release of this compiler. [EMISSION_MOD]
> use emission_mod
> --------^
> source/update_mod.f90(234): error #6404: This name does not have
> a type, and must have an explicit type. [HLEVXSECP]
> phXSec = xSecArray(j-IPnuP+1+HlevXSecP(__1)-1)
> ------------------------------__---------------------^
> source/update_mod.f90(238): error #6404: This name does not have
> a type, and must have an explicit type. [HEISINGXSECP]
> phXSec =
> xSecArray(j-IPnuP+1+__HeISingXSecP(1)-1)
> ------------------------------__---------------------^
> source/update_mod.f90(242): error #6404: This name does not have
> a type, and must have an explicit type. [HEIIXSECP]
> phXSec = xSecArray(j-IPnuP+1+HeIIXSecP(__1)-1)
> ------------------------------__---------------------^
> source/update_mod.f90(1304): error #6632: Keyword arguments are
> invalid without an explicit interface. [FILE_NAME]
> call
> equilibrium(file_name=__dataFile(elem, ion), &
> ------------------------------__------------^
> source/update_mod.f90(1305): error #6632: Keyword arguments are
> invalid without an explicit interface. [IONDENUP]
>
> &ionDenUp=ionDenUsed(__elementXref(elem),ion+1)/&
> ------------------------------__-^
> source/update_mod.f90(1306): error #6632: Keyword arguments are
> invalid without an explicit interface. [TE]
>
> &ionDenUsed(elementXref(elem),__ion), Te=TeUsed,&
> ------------------------------__------------------------------__------^
> source/update_mod.f90(1307): error #6632: Keyword arguments are
> invalid without an explicit interface. [NE]
> &Ne=NeUsed,
> FlineEm=forbiddenLinesLarge(&
> ------------------------------__-^
> source/update_mod.f90(1307): error #6632: Keyword arguments are
> invalid without an explicit interface. [FLINEEM]
> &Ne=NeUsed,
> FlineEm=forbiddenLinesLarge(&
> ------------------------------__------------^
> source/update_mod.f90(1310): error #6632: Keyword arguments are
> invalid without an explicit interface. [FILE_NAME]
> call
> equilibrium(file_name=__dataFile(elem, ion), &
> ------------------------------__------------^
> source/update_mod.f90(1311): error #6632: Keyword arguments are
> invalid without an explicit interface. [IONDENUP]
> &ionDenUp=0., Te=TeUsed,&
> ------------------------------__-^
> source/update_mod.f90(1311): error #6632: Keyword arguments are
> invalid without an explicit interface. [TE]
> &ionDenUp=0., Te=TeUsed,&
> ------------------------------__--------------^
> source/update_mod.f90(1312): error #6632: Keyword arguments are
> invalid without an explicit interface. [NE]
> &Ne=NeUsed,
> FlineEm=forbiddenLinesLarge(&
> ------------------------------__-^
> source/update_mod.f90(1312): error #6632: Keyword arguments are
> invalid without an explicit interface. [FLINEEM]
> &Ne=NeUsed,
> FlineEm=forbiddenLinesLarge(&
> ------------------------------__------------^
> source/update_mod.f90(2033): error #6404: This name does not
> have a type, and must have an explicit type. [RESLINE]
> do imul = 1, resLine(iL)%nmul
> ----------------------------^
> source/update_mod.f90(2033): error #6837: The leftmost part-ref
> in a data-ref can not be a function reference. [RESLINE]
> do imul = 1, resLine(iL)%nmul
> ----------------------------^
> source/update_mod.f90(2033): error #6158: The structure-name is
> invalid or is missing. [RESLINE]
> do imul = 1, resLine(iL)%nmul
> ----------------------------^
> source/update_mod.f90(2034): error #6837: The leftmost part-ref
> in a data-ref can not be a function reference. [RESLINE]
> if (resLine(iL)%elem==1) then
> ----------------------^
> source/update_mod.f90(2034): error #6158: The structure-name is
> invalid or is missing. [RESLINE]
> if (resLine(iL)%elem==1) then
> ----------------------^
> source/update_mod.f90(2034): internal error: Please visit
> 'http://www.intel.com/__software/products/support
> <http://www.intel.com/software/products/support>' for assistance.
> if (resLine(iL)%elem==1) then
> ^
> [ Aborting due to internal error. ]
> compilation aborted for source/update_mod.f90 (code 1)
> source/output_mod.f90(6): error #7013: This module file was not
> generated by any release of this compiler. [EMISSION_MOD]
> use emission_mod
> --------^
> source/output_mod.f90(342): error #6404: This name does not have
> a type, and must have an explicit type. [LOG10TE]
> log10Te = log10(TeUsed)
> -----------------------^
> source/output_mod.f90(343): error #6404: This name does not have
> a type, and must have an explicit type. [LOG10NE]
> log10Ne = log10(NeUsed)
> -----------------------^
> source/output_mod.f90(344): error #6404: This name does not have
> a type, and must have an explicit type. [SQRTEUSED]
> sqrTeUsed = sqrt(TeUsed)
> -----------------------^
> source/output_mod.f90(370): error #6410: This name has not been
> declared as an array or a function. [HIRECLINES]
> HIRecLines(iup, ilow) = &
> ------------------------------__--^
> source/output_mod.f90(370): internal error: Please visit
> 'http://www.intel.com/__software/products/support
> <http://www.intel.com/software/products/support>' for assistance.
> HIRecLines(iup, ilow) = &
> ^
> [ Aborting due to internal error. ]
> compilation aborted for source/output_mod.f90 (code 1)
> source/iteration_mod.f90(35): error #5102: Cannot open include
> file 'mpif.h'
> include 'mpif.h'
> -------------------^
> source/iteration_mod.f90(7): error #7013: This module file was
> not generated by any release of this compiler. [EMISSION_MOD]
> use emission_mod
> --------^
> source/iteration_mod.f90(103): error #6404: This name does not
> have a type, and must have an explicit type. [BJUMPTEMP]
> BjumpTemp = 0.
> -----------------^
> source/iteration_mod.f90(153): error #6404: This name does not
> have a type, and must have an explicit type. [MPI_REAL]
> & mpi_real, mpi_sum, mpi_comm_world, ierr)
> ------------------------^
> source/iteration_mod.f90(153): error #6404: This name does not
> have a type, and must have an explicit type. [MPI_SUM]
> & mpi_real, mpi_sum, mpi_comm_world, ierr)
> ------------------------------__----^
> source/iteration_mod.f90(153): error #6404: This name does not
> have a type, and must have an explicit type. [MPI_COMM_WORLD]
> & mpi_real, mpi_sum, mpi_comm_world, ierr)
> ------------------------------__-------------^
> source/iteration_mod.f90(477): error #6404: This name does not
> have a type, and must have an explicit type. [TOTALESCAPED]
> totalEscaped = 0.
> -----------^
> source/iteration_mod.f90(543): error #6632: Keyword arguments
> are invalid without an explicit interface. [ISTAR]
> call
> energyPacketDriver(iStar=0,n=__load, grid=grid(1:nGrids), &
> ------------------------------__--------------------------^
> source/iteration_mod.f90(543): error #6632: Keyword arguments
> are invalid without an explicit interface. [N]
> call
> energyPacketDriver(iStar=0,n=__load, grid=grid(1:nGrids), &
> ------------------------------__------------------------------__----^
> source/iteration_mod.f90(543): error #6632: Keyword arguments
> are invalid without an explicit interface. [GRID]
> call
> energyPacketDriver(iStar=0,n=__load, grid=grid(1:nGrids), &
> ------------------------------__------------------------------__------------^
> source/iteration_mod.f90(544): error #6632: Keyword arguments
> are invalid without an explicit interface. [GPLOC]
> & gpLoc=gpLoc, cellLoc=cellLoc)
> ------------------------------__---------^
> source/iteration_mod.f90(544): error #6632: Keyword arguments
> are invalid without an explicit interface. [CELLLOC]
> & gpLoc=gpLoc, cellLoc=cellLoc)
> ------------------------------__----------------------^
> source/iteration_mod.f90(546): error #6632: Keyword arguments
> are invalid without an explicit interface. [ISTAR]
> call
> energyPacketDriver(iStar=0,n=__load, grid=grid(1:nGrids), &
> ------------------------------__--------------------------^
> source/iteration_mod.f90(546): error #6632: Keyword arguments
> are invalid without an explicit interface. [N]
> call
> energyPacketDriver(iStar=0,n=__load, grid=grid(1:nGrids), &
> ------------------------------__------------------------------__----^
> source/iteration_mod.f90(546): error #6632: Keyword arguments
> are invalid without an explicit interface. [GRID]
> call
> energyPacketDriver(iStar=0,n=__load, grid=grid(1:nGrids), &
> ------------------------------__------------------------------__------------^
> source/iteration_mod.f90(547): error #6632: Keyword arguments
> are invalid without an explicit interface. [GPLOC]
> & gpLoc=gpLoc, cellLoc=cellLoc)
> ------------------------------__---------^
> source/iteration_mod.f90(547): error #6632: Keyword arguments
> are invalid without an explicit interface. [CELLLOC]
> & gpLoc=gpLoc, cellLoc=cellLoc)
> ------------------------------__----------------------^
> source/iteration_mod.f90(574): error #6404: This name does not
> have a type, and must have an explicit type. [MPI_INTEGER]
> & mpi_integer, mpi_sum, mpi_comm_world, ierr)
> ---------------------^
> compilation aborted for source/iteration_mod.f90 (code 1)
> source/mocassin.f90(43): error #5102: Cannot open include file
> 'mpif.h'
> include 'mpif.h'
> ------------^
> source/mocassin.f90(34): error #7002: Error in opening the
> compiled module file. Check INCLUDE paths. [DUST_MOD]
> use dust_mod
> --------^
> source/mocassin.f90(35): error #7013: This module file was not
> generated by any release of this compiler. [GRID_MOD]
> use grid_mod
> --------^
> source/mocassin.f90(55): error #6404: This name does not have a
> type, and must have an explicit type. [MPI_COMM_WORLD]
> call mpi_comm_rank(MPI_COMM_WORLD, taskid, ierr)
> -----------------------^
> compilation aborted for source/mocassin.f90 (code 1)
> make: *** [mocassin] Error 1
>
> The makefile is this:
>
> source1 = source/infnan.f90 source/constants_mod.f90
> source/vector_mod.f90 source/common_mod.f90
> source/interpolation_mod.f90 \
> source/set_input_mod.f90 source/hydro_mod.f90
> source/ph_mod.f90 source/composition_mod.f90 \
> source/continuum_mod.f90 source/ionization_mod.f90
> source/pathIntegration_mod.f90 \
> source/grid_mod.f90 source/dust_mod.f90
> source/emission_mod.f90 source/photon_mod.f90 \
> source/update_mod.f90 \
> source/output_mod.f90 source/iteration_mod.f90
> source/mocassin.f90
>
> source2 = source/infnan.f90 source/constants_mod.f90
> source/vector_mod.f90 source/common_mod.f90
> source/interpolation_mod.f90 \
> source/set_input_mod.f90 source/hydro_mod.f90
> source/ph_mod.f90 source/composition_mod.f90 \
> source/continuum_mod.f90 source/ionization_mod.f90
> source/pathIntegration_mod.f90 \
> source/grid_mod.f90 source/dust_mod.f90
> source/emission_mod.f90 source/photon_mod.f90 \
> source/update_mod.f90 \
> source/output_mod.f90 source/iteration_mod.f90
> source/mocassinWarm.f90
>
> source3 = source/infnan.f90 source/constants_mod.f90
> source/vector_mod.f90 source/common_mod.f90
> source/interpolation_mod.f90 \
> source/set_input_mod.f90 source/hydro_mod.f90
> source/ph_mod.f90 source/composition_mod.f90 \
> source/continuum_mod.f90 source/ionization_mod.f90
> source/pathIntegration_mod.f90 \
> source/grid_mod.f90 source/dust_mod.f90
> source/emission_mod.f90 source/photon_mod.f90 \
> source/update_mod.f90 \
> source/output_mod.f90 source/iteration_mod.f90
> source/mocassinOutput.f90
>
> source4 = source/infnan.f90 source/constants_mod.f90
> source/vector_mod.f90 source/common_mod.f90
> source/interpolation_mod.f90 \
> source/set_input_mod.f90 source/hydro_mod.f90
> source/ph_mod.f90 source/composition_mod.f90 \
> source/continuum_mod.f90 source/ionization_mod.f90
> source/pathIntegration_mod.f90 \
> source/grid_mod.f90 source/dust_mod.f90
> source/emission_mod.f90 source/photon_mod.f90 \
> source/update_mod.f90 \
> source/output_mod.f90 source/iteration_mod.f90
> source/mocassinPlot.f90
> F90 =
> /opt/intel/composer_xe_2011___sp1.6.233/composer_xe_2011___sp1.6.233/bin/intel64/ifort
> LIBS = -l/home/carol/mocassin/__mpich2install/include
> OPT1 = -O5
> OPT2 = -O5
>
> mocassin:
> $(F90) $(OPT1) -o mocassin $(source1) $(LIBS)
>
> mocassinWarm:
> $(F90) $(OPT1) -o mocassinWarm $(source2) $(LIBS)
>
> mocassinOutput:
> $(F90) $(OPT2) -o mocassinOutput $(source3) $(LIBS)
>
> mocassinPlot:
> $(F90) $(OPT2) -o mocassinPlot $(source4) $(LIBS)
>
> clean:
> /bin/rm *.o *~ *.mod mocassin mocassinWarm mocassinOutput
> mocassinPlot
>
> Does someone have a clue of what is the problem?
>
> Thanks,
> Carolina.
>
>
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