Hello,
Remove the -DMKL. This, I think, will make it look for MKL libraries, which
you aren't linking to (a blank MATH_LIBS line). Don't forget to do a make
clean before you retry the install.
Good luck,
Jason
On Fri, Dec 10, 2010 at 12:53 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> hi all
>
> I am trying to compile pmemd with gcc I was able to do it with intel
> compiler but with gcc I get the following error Warning: Obsolete:
> arithmetic IF statement at (1)
> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC veclib.fpp veclib.f90
> mpif90 -c -O3 veclib.f90
> mpicc -c pmemd_clib.c
> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC gb_alltasks_setup.fpp gb_alltasks_setup.f90
> mpif90 -c -O3 gb_alltasks_setup.f90
> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC pme_alltasks_setup.fpp pme_alltasks_setup.f90
> mpif90 -c -O3 pme_alltasks_setup.f90
> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC pme_setup.fpp pme_setup.f90
> mpif90 -c -O3 pme_setup.f90
> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC get_cmdline.fpp get_cmdline.f90
> mpif90 -c -O3 get_cmdline.f90
> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC master_setup.fpp master_setup.f90
> mpif90 -c -O3 master_setup.f90
> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC pmemd.fpp pmemd.f90
> mpif90 -c -O3 pmemd.f90
> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC erfcfun.fpp erfcfun.f90
> mpif90 -c -O3 erfcfun.f90
> mpif90 -o pmemd gbl_constants.o gbl_datatypes.o state_info.o
> file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o
> inpcrd_dat.o dynamics_dat.o img.o parallel_dat.o parallel.o
> gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o
> pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o
> bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o
> dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o
> loadbal.o shake.o prfs.o mol_list.o runmin.o constraints.o
> axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o
> runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o random.o degcnt.o
> erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o
> pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o
> nextprmtop_section.o -L/usr/mpi/gcc/openmpi-1.3.2-qlc/lib64
> gb_ene.o: In function `__gb_ene_mod__calc_born_radii':
> gb_ene.f90:(.text+0xe15): undefined reference to `vdinvsqrt_'
> gb_ene.f90:(.text+0x1174): undefined reference to `vdinv_'
> gb_ene.f90:(.text+0x118b): undefined reference to `vdinv_'
> gb_ene.f90:(.text+0x1287): undefined reference to `vdln_'
> gb_ene.f90:(.text+0x129e): undefined reference to `vdln_'
> gb_ene.o: In function `__gb_ene_mod__gb_ene':
> gb_ene.f90:(.text+0x29e7): undefined reference to `vdinv_'
> gb_ene.f90:(.text+0x2a72): undefined reference to `vdexp_'
> gb_ene.f90:(.text+0x2b61): undefined reference to `vdinvsqrt_'
> gb_ene.f90:(.text+0x2b94): undefined reference to `vdinvsqrt_'
> gb_ene.f90:(.text+0x344a): undefined reference to `vdinv_'
> gb_ene.f90:(.text+0x34c0): undefined reference to `vdexp_'
> gb_ene.f90:(.text+0x390c): undefined reference to `vdinvsqrt_'
> gb_ene.f90:(.text+0x3b37): undefined reference to `vdinv_'
> gb_ene.f90:(.text+0x3b4e): undefined reference to `vdinv_'
> gb_ene.f90:(.text+0x3bd7): undefined reference to `vdln_'
> collect2: ld returned 1 exit status
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory `/people/disk2/hbohr/amber10/src/pmemd/src'
> make: *** [all] Error 2
>
> my config.h file looks like this
>
>
> MATH_DEFINES =
> MATH_LIBS =
> MATH_DEFINES = -DMKL
> FFT_DEFINES = -DPUBFFT
> FFT_INCLUDE =
> FFT_LIBS =
> NETCDF_HOME =
> NETCDF_DEFINES =
> NETCDF_MOD =
> NETCDF_LIBS =
> MPI_HOME =/usr/mpi/gcc/openmpi-1.3.2-qlc
> MPI_DEFINES = -DMPI
> MPI_INCLUDE = -I$(MPI_HOME)/include
> MPI_LIBDIR = $(MPI_HOME)/lib64
> MPI_LIBS = -L$(MPI_LIBDIR)
> DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> CPP = /lib/cpp
> CPPFLAGS = -traditional -P
> F90_DEFINES = -DFFTLOADBAL_2PROC
>
> F90 = mpif90
> MODULE_SUFFIX = mod
> F90FLAGS = -c
> F90_OPT_DBG = -g -traceback
> F90_OPT_LO = -O0
> F90_OPT_MED = -O2
> F90_OPT_HI = -O3
> F90_OPT_DFLT = $(F90_OPT_HI)
>
> CC = mpicc
> CFLAGS =
>
> LOAD = mpif90
> LOADFLAGS =
>
> I have removed some of the optimization flags from the intel file.
>
> Have I removed too much?
>
> _______________________________________________
> 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
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Received on Fri Dec 10 2010 - 10:00:06 PST
