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Graphical idb error (not find start.s)

Sun, 08 Nov 2009 07:19:40 -0800

I'm using intel fortran 11.1.056 on Ubuntu 9.10

If I compile with -g option and run with idb in graphic mode

it said as follows.

Unable to locate source file "/build/buildd/eglibc-2.10.1/sysdeps/x86_64/elf/start.S"
Do you like to search for it manually?

Is there any solution to solve this problem ?

error #8032: Generic procedure reference has two or more specific procedure with the same type/rank/keyword signature

Sat, 07 Nov 2009 16:43:41 -0800

Hi,

I am trying to compile my code on a linux platform, migrating from an IRIX box that served me faithfully for the last 7-8 years.

When compling the code below, (I show only the relevant part), using the following compiler options:

mpif90 -std -fpconstant -g -traceback -debug -O0 -fpe0 -check_bounds gs_module.f90

I get these warnings and then errors:

gs_module.f90(14): warning #6738: The type/rank/keyword signature for this specific procedure matches another specific procedure that shares the same generic-name.   [SCATTER_MODULE^MAX_SCATTER_VECTOR_DOUBLE]
use scatter_module, only: SUM_SCATTER, MIN_SCATTER, MAX_SCATTER, OR_SCATTER
------^
gs_module.f90(258): error #8032: Generic procedure reference has two or more specific procedure with the same type/rank/keyword signature.   [GATHER]
call gather (Dest, Src, Mesh, TYPE = EE, TRACE = EE_TRACE, &
---------^
gs_module.f90(293): error #8032: Generic procedure reference has two or more specific procedure with the same type/rank/keyword signature.   [GATHER]
call gather (Dest, Src, Mesh, TYPE = EE, TRACE = EE_TRACE, &
---------^

I would welcome any solution to this compiling error (I care less about the warnings).

Thanks,

Adrian

MODULE GS_MODULE
!=======================================================================
! Purpose(s):
!
!   Define the interfaces and global variables
!   for the gather/scatter support
!
!=======================================================================
use gather_module, only: GATHER
use gs_info_module, only: EN_TRACE, EE_TRACE, EN, EE
use kind_module,    only: log_kind
use parameter_module
use scatter_module, only: SUM_SCATTER, MIN_SCATTER, MAX_SCATTER, OR_SCATTER
implicit none
! Private Module
private
! Public procedures
Public :: EE_Gather, EN_Gather, EN_MIN_Gather, EN_MAX_Gather, EN_OR_Gather, &
EN_SUM_Scatter, EN_MIN_Scatter, EN_MAX_Scatter, EN_OR_Scatter,    &
EE_GS_INIT, EN_GS_INIT
! Arrays and variables used only inside this module
logical(KIND = log_kind), save, private, pointer, dimension(:,:) :: El_Nbr_MASK
logical(KIND = log_kind), save, private :: EE_MASK_Initialized = .false.
! <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
! Interface blocks
INTERFACE EE_GATHER
!=======================================================================
! Purpose -
!   Gather integer cell-centered data from cell face neighbors
!   into a integer cell-centered vector of length nfc
!
!    Input:
!          Mesh - Mesh connectivity structure
!          Src - Cell-centered quantity
!   Output:
!          Dest - Cell-centered vector of length nfc containing
!                 the value of Src for all face neighbor cells
!
!=======================================================================
MODULE PROCEDURE EE_GATHER_INT
MODULE PROCEDURE EE_GATHER_SINGLE
MODULE PROCEDURE EE_GATHER_DOUBLE
END INTERFACE
!========== EE_GATHER_INT========================================
! This is included by gs_module for the top level gather routines.
! This is the parallel version
SUBROUTINE EE_GATHER_INT (Dest, Src, BOUNDARY)
!=======================================================================
! PURPOSE -
!
!=======================================================================
use gs_info_module, only: EE_TRACE, EE
use kind_module
use mesh_module,    only: Mesh
use pgslib_module, only: PGSLib_GS_Trace_Setup_P
implicit none
! Incoming Arguments
integer (int_kind) , intent(IN   ),                               &
dimension (ncells)                              :: Src
integer (int_kind) , intent( OUT),                               &
dimension (nfc,ncells)                              :: Dest
integer (int_kind) , dimension (:),                             &
POINTER,                                     &
OPTIONAL                                     :: BOUNDARY
! Local Variables
! <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
! Initialize relevant quantities
Dest = 0_int_kind
IF (.NOT. EE_MASK_Initialized) then
EE_MASK_Initialized = .true.
call gs_init_ee_mask()
END IF
IF (.NOT. PGSLib_GS_Trace_Setup_P(EE_Trace)) Call EE_GS_Init()
call gather (Dest, Src, Mesh, TYPE = EE, TRACE = EE_TRACE, &
MASK = El_Nbr_Mask, BOUNDARY = BOUNDARY)
return
END SUBROUTINE EE_GATHER_INT
!========== EE_GATHER_SINGLE========================================
! This is included by gs_module for the top level gather routines.
! This is the parallel version
SUBROUTINE EE_GATHER_SINGLE (Dest, Src, BOUNDARY)
!=======================================================================
! PURPOSE -
!
!=======================================================================
use gs_info_module, only: EE_TRACE, EE
use kind_module
use mesh_module,    only: Mesh
use pgslib_module, only: PGSLib_GS_Trace_Setup_P
implicit none
! Incoming Arguments
real (single_kind) , intent(IN   ),                               &
dimension (ncells)                              :: Src
real (single_kind) , intent( OUT),                               &
dimension (nfc,ncells)                              :: Dest
real (single_kind) , dimension (:),                             &
POINTER,                                     &
OPTIONAL                                     :: BOUNDARY
! Local Variables
! <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
! Initialize relevant quantities
Dest = 0.0_single_kind
IF (.NOT. EE_MASK_Initialized) then
EE_MASK_Initialized = .true.
call gs_init_ee_mask()
END IF
IF (.NOT. PGSLib_GS_Trace_Setup_P(EE_Trace)) Call EE_GS_Init()
call gather (Dest, Src, Mesh, TYPE = EE, TRACE = EE_TRACE, &
MASK = El_Nbr_Mask, BOUNDARY = BOUNDARY)
return
END SUBROUTINE EE_GATHER_SINGLE
!========== EE_GATHER_DOUBLE========================================
! This is included by gs_module for the top level gather routines.
! This is the parallel version
SUBROUTINE EE_GATHER_DOUBLE (Dest, Src, BOUNDARY)
!=======================================================================
! PURPOSE -
!
!=======================================================================
use gs_info_module, only: EE_TRACE, EE
use kind_module
use mesh_module,    only: Mesh
use pgslib_module, only: PGSLib_GS_Trace_Setup_P
implicit none
! Incoming Arguments
real (double_kind) , intent(IN   ),                               &
dimension (ncells)                              :: Src
real (double_kind) , intent( OUT),                               &
dimension (nfc,ncells)                              :: Dest
real (double_kind) , dimension (:),                             &
POINTER,                                     &
OPTIONAL                                     :: BOUNDARY
! Local Variables
! <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
! Initialize relevant quantities
Dest = 0.0_double_kind
IF (.NOT. EE_MASK_Initialized) then
EE_MASK_Initialized = .true.
call gs_init_ee_mask()
END IF
IF (.NOT. PGSLib_GS_Trace_Setup_P(EE_Trace)) Call EE_GS_Init()
call gather (Dest, Src, Mesh, TYPE = EE, TRACE = EE_TRACE, &
MASK = El_Nbr_Mask, BOUNDARY = BOUNDARY)
return
END SUBROUTINE EE_GATHER_DOUBLE

END MODULE GS_MODULE

=================

the other module where gather is defined

MODULE GATHER_MODULE
!=======================================================================
! PURPOSE -
!   Routines for gather. These are used by both
!   Element<->Element and Element<->Node.
!
!=======================================================================
use gs_info_module
use pgslib_module,     ONLY: PGSLib_GS_Struct, PGSLib_Gather_Buffer

implicit none
save
public :: Gather
! Interface blocks
INTERFACE Gather
!=======================================================================
! PURPOSE -
!   Gather either cell-centered data or vertex centered data
!   into a cell-centered vector of length ShortDim
!
!    Input:
!          Mesh - Mesh connectivity structure
!          Src - Cell or vertex -centered quantity
!   Output:
!          Dest - Cell-centered vector of length ShortDim containing
!                 the value of Src for all neighbors
!
!=======================================================================
MODULE PROCEDURE Gather_INT
MODULE PROCEDURE Gather_SINGLE
MODULE PROCEDURE Gather_DOUBLE
END INTERFACE
! <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
CONTAINS
!=======================================================================
! PURPOSE -
!   Gather either cell-centered data or vertex centered integer data
!   into an integer cell-centered vector of length ShortDim
!=======================================================================
SUBROUTINE GATHER_INT (Dest, Src, Mesh, TYPE, TRACE, BOUNDARY, MASK)
!=======================================================================
! PURPOSE -
!   Gather either cell-centered data or vertex centered integer data
!   into a integer (int_kind) cell-centered vector of length ShortDim
!=======================================================================
use error_module, only: PUNT
use kind_module
use mesh_module, only: MESH_CONNECTIVITY, CllNgbr, Vrtx
implicit none
! Arguments
integer (int_kind)             , dimension(:,:),                        &
intent(OUT)                            :: Dest
integer (int_kind)             , dimension(:),                          &
intent(IN)                             :: Src
type(MESH_CONNECTIVITY), dimension(SIZE(Dest,2)),               &
intent(IN)                             :: Mesh
integer (int_kind)             , dimension(:),                          &
POINTER,                               &
OPTIONAL                               :: BOUNDARY
logical(KIND = log_kind), dimension(SIZE(Dest,1), SIZE(Dest,2)), &
intent(IN ),                           &
OPTIONAL                               :: MASK
type (COMM_TYPE),         intent(IN   )                          :: TYPE
type (PGSLib_GS_Struct), intent(IN) :: Trace
! Local scalars & arrays
integer(KIND = int_kind) :: f, c
logical(KIND = log_kind) :: PRESENT_MASK, TEMP_BOUNDARY, NEW_BOUNDARY
integer (int_kind),        POINTER,         dimension(:) :: Supplement_Data
integer (int_kind),        dimension(Trace%N_Duplicate) :: Duplicate_Data
! <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
! Initialize relevant quantities
PRESENT_MASK = PRESENT(MASK)
! If BOUNDARY is not passed in, then we have to use a local
! boundaray. If BOUNDARY is passed in, then if it is NULL
TEMP_BOUNDARY = .NOT. PRESENT(BOUNDARY)
! If the BOUNDARY is associated, use it, otherwise get new boundary data.
IF (TEMP_BOUNDARY) THEN
NEW_BOUNDARY   = .TRUE.
ELSE
NEW_BOUNDARY   = .NOT. ASSOCIATED(BOUNDARY)
ENDIF
IF (NEW_BOUNDARY) THEN
ALLOCATE(Supplement_Data(Trace%N_Supplement))
IF (.NOT. TEMP_BOUNDARY) BOUNDARY => Supplement_Data
! Gather into comm buffer
Duplicate_Data = Src(Trace%Duplicate_Indices)
ELSE
! If we were passed in a boundary, and it was allocated already,
! then us it
IF (.NOT. TEMP_BOUNDARY) Supplement_Data => BOUNDARY
END IF

IF (TEMP_BOUNDARY) DEALLOCATE(Supplement_Data)
return
END SUBROUTINE GATHER_INT

!=======================================================================
! PURPOSE -
!   Gather either cell-centered data or vertex centered single data
!   into a single cell-centered vector of length ShortDim
!=======================================================================
! This is included for the gather routines.
! This is the parallel version
SUBROUTINE GATHER_SINGLE (Dest, Src, Mesh, TYPE, TRACE, BOUNDARY, MASK)
!=======================================================================
! PURPOSE -
!   Gather either cell-centered data or vertex centered integer data
!   into a real (single_kind) cell-centered vector of length ShortDim
!=======================================================================
use error_module, only: PUNT
use kind_module
use mesh_module, only: MESH_CONNECTIVITY, CllNgbr, Vrtx
implicit none
! Arguments
real (single_kind)             , dimension(:,:),                        &
intent(OUT)                            :: Dest
real (single_kind)             , dimension(:),                          &
intent(IN)                             :: Src
type(MESH_CONNECTIVITY), dimension(SIZE(Dest,2)),               &
intent(IN)                             :: Mesh
real (single_kind)             , dimension(:),                          &
POINTER,                               &
OPTIONAL                               :: BOUNDARY
logical(KIND = log_kind), dimension(SIZE(Dest,1), SIZE(Dest,2)), &
intent(IN ),                           &
OPTIONAL                               :: MASK
type (COMM_TYPE),         intent(IN   )                          :: TYPE
type (PGSLib_GS_Struct), intent(IN) :: Trace
! Local scalars & arrays
integer(KIND = int_kind) :: f, c
logical(KIND = log_kind) :: PRESENT_MASK, TEMP_BOUNDARY, NEW_BOUNDARY
real (single_kind),        POINTER,         dimension(:) :: Supplement_Data
real (single_kind),        dimension(Trace%N_Duplicate) :: Duplicate_Data
! <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
! Initialize relevant quantities
PRESENT_MASK = PRESENT(MASK)
! If BOUNDARY is not passed in, then we have to use a local
! boundaray. If BOUNDARY is passed in, then if it is NULL
TEMP_BOUNDARY = .NOT. PRESENT(BOUNDARY)
! If the BOUNDARY is associated, use it, otherwise get new boundary data.
IF (TEMP_BOUNDARY) THEN
NEW_BOUNDARY   = .TRUE.
ELSE
NEW_BOUNDARY   = .NOT. ASSOCIATED(BOUNDARY)
ENDIF
IF (NEW_BOUNDARY) THEN
ALLOCATE(Supplement_Data(Trace%N_Supplement))
IF (.NOT. TEMP_BOUNDARY) BOUNDARY => Supplement_Data
! Gather into comm buffer
Duplicate_Data = Src(Trace%Duplicate_Indices)
ELSE
! If we were passed in a boundary, and it was allocated already,
! then us it
IF (.NOT. TEMP_BOUNDARY) Supplement_Data => BOUNDARY
END IF

IF (TEMP_BOUNDARY) DEALLOCATE(Supplement_Data)
return
END SUBROUTINE GATHER_SINGLE

END MODULE GATHER_MODULE

Install under Slackware64 13

Fri, 06 Nov 2009 16:12:53 -0800

Hi Forum

I want to Install the noncommercial version of icc/ifort and mkl in my Slakware box, so far I have been using the -norpm flag with Install.sh script, It shows the install options ment, defaulting to show the license agreement, which i accept, and exits to shell instead of continuing...

... What must i do to have the Intel Development suite installed in my Slack...?

BRGDS

Alex

Epoch to Calendar

Fri, 06 Nov 2009 14:29:30 -0800

I have been trying to write my own converter that allows me to convert from epoch seconds to YYYYMMDD. Not going well. My question is there a converter in fortran that will do this for me? Or does someone have a code line that works?

performance penalty for -fPIC, -shared, or derived data types?

Fri, 06 Nov 2009 12:54:30 -0800

Hello,

I have two chunks of code here that are reading the same ~800 MB unformatted binary file. The file in question is sequentially-accessed and has variable record lengths. Both codes are compiled at the same optimization level with the 11.1 version of the Intel Fortran compiler. Both codes have something to the effect of:

write(*,*) "reading"
do g1=1,igm
do k1=1,km
read(read_unit) data(file)%flux_3d(g1,:,:,k1)
enddo
enddo
write(*,*) "done reading"

However, one code appears to be completing this operation about 10-20 times faster than the other. (Determined using a series of unscientific "stopwatch" tests.) The one that seems to be moving more slowly is compiled with -fPIC, loaded into a shared object, and reads the data into a derived type. Could any of this be causing the performance discrepancy, or is something else probably at work here?

Thanks,
Greg

undefined symbols problem

Fri, 06 Nov 2009 10:18:50 -0800

Hi, I am using Intel Fortran v11.0.67 on a Mac with OS 10.5.8, and gcc version 4.0.1 (Apple Inc. build 5493). I recently installed MPICH with your help (thanks again!) to run a code that requires MPI although it is actually running on a single processor. The makefile for this code is given at the end of this message (sorry but I couldnt figure out how to upload it).

The problem I am having is that the subroutines and modules compile OK, but then I get the following error messages:

Undefined symbols:
"_amr_1blk_guardcell_srl_", referenced from:
_amr_1blk_guardcell_ in mpi_amr_1blk_guardcell.o
_amr_1blk_guardcell_ in mpi_amr_1blk_guardcell.o
"_amr_1blk_cc_prol_gen_work_fun_", referenced from:
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_amr_prolong_ in mpi_amr_prolong.o
"_amr_1blk_cc_prol_gen_unk_fun_", referenced from:
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_amr_prolong_ in mpi_amr_prolong.o
"_amr_1blk_fc_prol_gen_fun_", referenced from:
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_mpi_amr_1blk_guardcell_c_to_f_ in mpi_amr_1blk_guardcell_c_to_f.o
_amr_prolong_ in mpi_amr_prolong.o
_amr_prolong_ in mpi_amr_prolong.o
_amr_prolong_ in mpi_amr_prolong.o
ld: symbol(s) not found

The "undefined symbols" are subroutine names, but the subroutines themselves have been compiled successfully (you can see them listed in the makefile, and I checked the compile output to make sure the object files were created). I found somewhat similar problems in earlier Forum postings, but no answers that were sufficiently general to provide a solution for me. If you could point me in the right direction to determine what is going on, I'd be most grateful!

regards, Judy K
----------------------------makefile below-------------------
# This makefile was designed to compile a users application with
# the amr package on an Intel processor. The amr package is assumed to
# be located in a sub-directory tree rooted at the sub-directory
# specified as AMRDIR below. The amr source files are assumed to
# be in the sub-directory AMRDIR/source and the required header
# files in AMRDIR/headers. The users own application source and
# headers files are assumed to be in the same sub-directory as
# this makefile.

# specify path to amr top directory                             USER EDIT
AMRDIR = ..

# define the application specific object files required         USER EDIT
APP_OBJS= loop_coarse.nosh.o\
area_subs_uniform.nosh.o \
output_soln_area.nosh.o \
read_dump.nosh.o \
dump_for_restart.nosh.o \
nthermal_area.jakrad.nosh.o \
ntrislv.nosh.o \
nadvect_muscl_area.lesh.o \
ninitial_muscl_area.jtknosh.o \
solar_initial.nosh.o \
muscl_lib_area.nosh.o \
ngravity_lookup.nosh.o \
cfd1d_area.nosh.o \
rieman04_area.nosh.o \
amr_bc_block.nosh.o \
amr_1blk_bcset_area.nosh.o \
rheapsort.nosh.o \
amr_test_refinement.nosh.o

# list of modules required by the code
APP_MODULES= \
paramesh_dimensions.o \
paramesh_interfaces.o \
physicaldata.o \
prolong_arrays.o \
timings.o \
tree.o \
workspace.o \
io.o \
constants.o \
paramesh_comm_data.o \
mpi_morton.o \
paramesh_mpi_interfaces.o \
module_constants.o \
module_gravtable.o \
module_loopparams.o \
module_padded_block.o \
module_pointers.o \
accel.o \
storage.o
# module_tracer.o
# module_workspace.o \
# module_amr_shmem.o \
# module_shmem_reduce.o \
# module_physicaldata.o \
# module_tree.o \

# sets the list of object files needed from the amr source - DO NOT ALTER
AMR_OBJS= \
amr_1blk_cc_cp_remote.o \
amr_1blk_cc_prol_gen_unk_fun.o \
amr_1blk_cc_prol_inject.o \
amr_1blk_cc_prol_linear.o \
amr_1blk_cc_prol_genorder.o \
amr_1blk_cc_prol_user.o \
amr_1blk_cc_prol_gen_work_fun.o \
amr_1blk_cc_prol_work_inject.o \
amr_1blk_cc_prol_work_linear.o \
amr_1blk_cc_prol_work_genorder.o \
amr_1blk_cc_prol_work_user.o \
amr_1blk_copy_soln.o    \
amr_1blk_ec_cp_remote.o \
amr_1blk_ec_prol_gen_fun.o \
amr_1blk_ec_prol_genorder.o \
amr_1blk_ec_prol_user.o \
amr_1blk_ec_prol_linear.o \
amr_1blk_fc_prol_dbz.o \
clean_field.o \
poisson_sor.o \
amr_1blk_fc_clean_divb.o \
amr_1blk_fc_cp_remote.o \
amr_1blk_fc_prol_gen_fun.o \
amr_1blk_fc_prol_inject.o \
amr_1blk_fc_prol_linear.o \
amr_1blk_fc_prol_genorder.o \
amr_1blk_fc_prol_user.o \
amr_1blk_guardcell_reset.o \
amr_1blk_guardcell_srl.o \
set_f2c_indexes.o \
amr_1blk_nc_cp_remote.o \
amr_1blk_nc_prol_gen_fun.o \
amr_1blk_nc_prol_genorder.o \
amr_1blk_nc_prol_user.o \
amr_1blk_nc_prol_linear.o \
amr_1blk_save_soln.o \
amr_1blk_t_to_perm.o \
amr_1blk_to_perm.o \
amr_bcset_init.o \
amr_block_geometry.o \
user_coord_transfm.o \
amr_close.o \
amr_initialize.o \
amr_set_runtime_parameters.o \
amr_mpi_find_blk_in_buffer.o \
amr_perm_to_1blk.o \
amr_prolong_cc_fun_init.o \
amr_prolong_face_fun_init.o \
amr_prolong_fun_init.o \
amr_reorder_grid.o \
amr_restrict_ec_fun.o \
amr_restrict_ec_genorder.o \
amr_restrict_ec_user.o \
amr_restrict_edge.o \
amr_restrict_fc_fun.o \
amr_restrict_fc_genorder.o \
amr_restrict_fc_user.o \
amr_restrict_red.o \
amr_restrict_unk_fun.o \
amr_restrict_unk_genorder.o \
amr_restrict_unk_user.o \
amr_restrict_nc_fun.o \
amr_restrict_nc_user.o \
amr_restrict_nc_genorder.o \
amr_restrict_work_fun.o \
amr_restrict_work_genorder.o \
amr_restrict_work_user.o \
amr_restrict_work_fun_recip.o \
amr_system_calls.o \
amr_q_sort.o \
amr_q_sort_real.o \
mpi_amr_singular_line.o \
mpi_amr_1blk_guardcell.o \
mpi_amr_1blk_guardcell_c_to_f.o \
mpi_amr_1blk_restrict.o \
mpi_amr_comm_setup.o \
mpi_amr_edge_average.o \
mpi_amr_edge_average_udt.o \
mpi_amr_edge_average_vdt.o \
mpi_amr_edge_diagonal_check.o \
mpi_amr_flux_conserve.o \
mpi_amr_flux_conserve_udt.o \
mpi_amr_flux_conserve_vdt.o \
mpi_amr_get_remote_block.o \
mpi_amr_get_remote_block_fvar.o \
mpi_amr_global_domain_limits.o \
mpi_amr_guardcell.o \
mpi_amr_local_surr_blks_lkup.o \
mpi_amr_prolong.o \
mpi_amr_prolong_fc_divbconsist.o \
mpi_amr_refine_derefine.o \
amr_morton_process.o \
local_tree.o \
find_surrblks.o \
local_tree_build.o \
tree_search_for_surrblks.o \
mpi_amr_restrict.o \
mpi_amr_restrict_fulltree.o \
mpi_amr_restrict_bnd_data_vdt.o \
mpi_amr_restrict_edge_data_vdt.o \
mpi_amr_store_comm_info.o \
mpi_amr_timing_report.o \
mpi_amr_tree_setup.o \
mpi_get_buffer.o \
mpi_get_edge_buffer.o \
mpi_get_flux_buffer.o \
mpi_morton_bnd.o \
process_fetch_list.o \
compress_fetch_list.o \
mpi_morton_bnd_fluxcon.o \
mpi_morton_bnd_prolong.o \
mpi_morton_bnd_restrict.o \
mpi_pack_blocks.o \
mpi_unpack_blocks.o \
mpi_put_buffer.o \
mpi_pack_edges.o \
mpi_pack_fluxes.o \
mpi_put_edge_buffer.o \
mpi_put_edge_buffer_1blk.o \
mpi_put_flux_buffer.o \
mpi_set_message_limits.o \
mpi_set_message_sizes.o \
mpi_unpack_edges.o \
mpi_unpack_fluxes.o \
rationalize_fetch_list.o \
mpi_amr_checkpoint_wr.o \
mpi_amr_checkpoint_re.o \
mpi_amr_checkpoint_wr_default.o \
mpi_amr_checkpoint_re_default.o \
mpi_amr_checkpoint_wr_hdf5.o \
mpi_amr_checkpoint_re_hdf5.o \
mpi_amr_checkpoint_wr_mpiio.o \
mpi_amr_checkpoint_re_mpiio.o \
read_blocks_hdf5_r4.o \
read_blocks_hdf5_r8.o \
write_blocks_hdf5_r4.o \
write_blocks_hdf5_r8.o \
mpi_amr_plotfile_chombo.o \
write_blocks_chombo_r4.o \
write_blocks_chombo_r8.o \
mpi_amr_derefine_blocks.o \
mpi_amr_check_derefine.o \
amr_morton_order.o \
amr_compute_morton.o \
amr_sort_morton.o \
amr_sort_morton_reorder_grid.o \
amr_sort_by_work.o \
amr_migrate_tree_data.o \
fill_old_loc.o \
morton_sort.o \
mpi_amr_redist_blk.o \
send_block_data.o \
mpi_amr_refine_blocks.o \
amr_check_refine.o \
mpi_amr_restrict_bnd_data.o \
mpi_amr_restrict_edge_data.o \
mpi_amr_boundary_block_info.o \
mpi_amr_test_neigh_values.o \
mpi_lib.o \
mpi_pack_tree_info.o \
mpi_unpack_tree_info.o \
mpi_wrapper_int.o \
mpi_wrapper_logical.o \
mpi_wrapper_real.o \
mpi_wrapper_dble.o \
namr_shmem_lib_1proc.o

.SUFFIXES : .F90 .c .F .f .o

.F90.o :
$(FC) $(FFLAGS) -c $<
.F.o :
$(FC) $(FFLAGS) -c $<
.f.o :
$(FC) $(FFLAGS) -c $<
.c.o :
$(CC) $(CFLAGS) -c $<

# Tunable parameters
#
# FC        Name of the fortran compiling system to use
# CC            Name of C compiler
# LDFLAGS    Flags to the loader
# LIBS        List of libraries
# CMD        Name of the executable
# PROFLIB    Library needed for profiling
#--------------------------
# For running on the intel fortran compiler
#FC = ifort
FC = mpif90
CC = mpicc
#----------------------
LIBS =
CMD =        condense
PROFLIB =

#for intel fortran compiler.
FFLAGS = -w -fpp1 -axSSSE3 -O3 -pad -align -prefetch -r8 -rdynamic
#for g95 fortran compiler.
#FFLAGS = -O3 -r8 -i4 -fbounds-check -ftrace=full

# for gcc compiler
CFLAGS = -O -I../headers

#    USER EDIT

# end test
#----------------------------------------------------------

# Lines from here on down should not need to be changed. They are the
# actual rules which make uses to build the command
#
shmem:        $(CMD)

$(CMD):        $(APP_MODULES) $(AMR_OBJS) $(APP_OBJS)
$(FC) $(LDFLAGS) -o $(@) $(APP_MODULES) $(APP_OBJS) $(AMR_OBJS) $(LIBS)

$(AMR_OBJS): $(APP_MODULES)
$(APP_OBJS): $(APP_MODULES)

clean:
@rm -f *.o

Problem while installing the Product for IA-32/Intel® 64

Fri, 06 Nov 2009 03:57:16 -0800

Following messages have come while installing the intel fortran compile.

"Missing optional pre-requisites
-No compatible java* Runtime Environment (JRE) found'.

Even I have installed the JRE ( jre-1.5.0_06) and the path of the jre is included in .bashrc file, I am receiving the same above message while installing the fortran compiler.

I need advice for solving this problem.

with kind regards
R.K. nayak

ifort produces different binaries from the same source at two diffrent timepoints

Fri, 06 Nov 2009 03:06:14 -0800

Hello,

I use ifort in conjunction with -fpp flag since there is some preprocessing in the code. The preprocessing directives are all of #ifndef #endif type, to include or exclude pieces of code according to my desires.

I have noticed that with -fpp, each time I compile the code I get a different executable. This was checked by using cmp compand on Linux.
Without preprocessing, the produced binaries are identical.

To be completely precise,I compare, of course, preprocessed to preprocessed instances, and the same for non-preprocessed.

What could be the reason for the differences, when the code, optimisation et al. is always the same?

The compiler version is 10.1, and it works on a Linux cluster (i don't have all the specific details for the platform, if requested i'll bother the cluster support guys)

Yet another stack overflow...

Fri, 06 Nov 2009 01:20:00 -0800

Hello people!

I am using Debian Linux with te ifort version 10.1 and am developing a procedure for scientific purposes that explores a cluster of elements on some sort of a mathematical graph and extracts some information about that cluster. The procedure is recursive and it works fine up till some limiting size of the cluster (about 500000 elements in the cluster). When the size is exceeded the stack overflows and the program breaks. I am aware that it has to break at some point and I am fine with that, but what I do not understand is the fact that I can not postpone this ocurrence. What it says is:

"forrtl: severe (174): SIGSEGV, segmentation fault occurred"

I first I have reduced considerably the variables in the recusrsive procedure and it did not help at all, secondly I have tried to send instructions to "ld" to increase stack size by including a switch "-Xlinker --stack xxx" in the ifort command and it said "ld: unrecognized option '--stack'" which is curious since that switch can be found in the man pages of ld. The third thing I tried is using "ulimit -s unlimited" command and hence increased the stack size within bash - still no help to my problem. And one more thing, I am pretty sure that none of my integer variables exceed their max values.

The curious thing is that the program uses the same amount of ram in all the cases which is much less (150mb) than the amount of ram on my computer at the time it breaks. I wonder why does he not allocate the additional ram if he needs it? I was wondering if somebody has some insight in the way the recursive subroutines compile with ifort and has a solution of some sort. Remember, I do not need magic, I just want it to break because it has no more ram available if it has to break because of something :). I would rather not have to decompose the thing in do loops if I can somehow increase the available memory by manipulating ifort and/or linker commands.

Thanks very much in advance, Ivan Balog.

Segfault on stdout OR terminal output WRITE(6,*) ??

Thu, 05 Nov 2009 15:36:25 -0800

I am a fairly experienced fortran programmer, but I have never seen this before. Probably because the implimentation here is a little slapped-together, and for a full-fledged project things would be different. Here is the problem:

I have a fairly small optimization routine, in fortran, that is compiled by commands from a perl script. Ultimately this fortran routine is run and the output (a series of WRITE(6,*)) is read in by the perl script through a basic $values = `./a.out stuff...` type command. THis has been working fine for weeks.

I changed a few things (more outputs), and now the program segfaults, seemingly at random (anywhere from 3 - 30 loops will go by running the system command just fine and then one will fail)

WRITE(12,'(/,'' **** RESULTS AFTER SA **** '')')
CALL PRTVEC(XOPT,N,'SOLUTION')
WRITE(12,'(A)')'THIS TEXT DOES NOT CAUSE PROBLEM'
CALL PRTVEC(VM,N,'FINAL STEP LENGTH')
WRITE(12,'(A)')'NOR THIS'
WRITE(12,1001) FOPT, NFCNEV, NACC, NOBDS, T, IER

1000 FORMAT(/,' SIMULATED ANNEALING EXAMPLE',/,&
/,' NUMBER OF PARAMETERS: ',I3,' MAXIMAZATION: ',L5,&
/,' INITIAL TEMP: ', G8.2, ' RT: ',G8.2, ' EPS: ',G8.2,&
/,' NS: ',I3, ' NT: ',I2, ' NEPS: ',I2,&
/,' MAXEVL: ',I10, ' IPRINT: ',I1, ' ISEED1: ',I4,&
' ISEED2: ',I4)
1001 FORMAT(/,' OPTIMAL FUNCTION VALUE: ',G20.13&
/,' NUMBER OF FUNCTION EVALUATIONS: ',I10,&
/,' NUMBER OF ACCEPTED EVALUATIONS: ',I10,&
/,' NUMBER OF OUT OF BOUND EVALUATIONS: ',I10,&
/,' FINAL TEMP: ', G20.13,' IER: ', I3)
WRITE(6,'(I5,X)', ADVANCE='no')CL_INT1
WRITE(6,'(I5,X)', ADVANCE='no')CL_INT2
WRITE(6,'(A)')''

These WRITE(6) statements never get written, and if the fortran is executed from inside the perl I never even hear the error message - it just hangs and when I kill it a.out is still running in the background doing nothing! It just sits! If I take it out on it's own and run it, I get this:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libc.so.6 00007FF84A607E5D Unknown Unknown Unknown
libc.so.6 00007FF84A60A4C9 Unknown Unknown Unknown
libc.so.6 00007FF84A60C7EE Unknown Unknown Unknown
libc.so.6 00007FF84A6648E5 Unknown Unknown Unknown
a.out 000000000044F387 Unknown Unknown Unknown
a.out 000000000041F385 Unknown Unknown Unknown
a.out 000000000043B537 Unknown Unknown Unknown
a.out 0000000000408047 Unknown Unknown Unknown
a.out 000000000040396C Unknown Unknown Unknown
libc.so.6 00007FF84A5B0ABD Unknown Unknown Unknown
a.out 0000000000403869 Unknown Unknown Unknown

I have NO IDEA why this is happening, and all my usual tricks to find where Fortran is unhappy are failing. And this shouldn't be using THAT much memory. The only big thing is the output from the subroutine 'SA' which will happily write a thousand megabyte log file. I don't know if this is related, it hadn't been a problem so far.