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pio build too slowly

zdliu

zdliu

Member
Hi,
when I bulid one case by CESM104, and its pio bulidexe is so slowly, almost half an hour (clock time: 01:05:02 ==> 01:42:12 ), and FINISHED SUCCESSFULLY however.
and in the file pio.bldlog.*, there are so many repeated lines "Making dependencies for *.F90 --> *.d" (40000 lines repeated!)So what happend? What is wrong?Thanks in advance. zliu--------------------------------------------------------------------
 CCSM BUILDEXE SCRIPT STARTING
 - Build Libraries: mct pio csm_share
Sat Apr 18 01:04:15 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/bld/mct/mct.bldlog.150418-010411
Sat Apr 18 01:05:02 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/bld/pio/pio.bldlog.150418-010411
Sat Apr 18 01:42:12 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/bld/csm_share/csm_share.bldlog.150418-010411
Sat Apr 18 01:43:05 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/run/cpl.bldlog.150418-010411
Sat Apr 18 01:43:05 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/run/atm.bldlog.150418-010411
Sat Apr 18 01:48:54 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/run/lnd.bldlog.150418-010411
Sat Apr 18 01:55:24 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/run/ice.bldlog.150418-010411
Sat Apr 18 01:56:32 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/run/ocn.bldlog.150418-010411
Sat Apr 18 01:59:32 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/run/glc.bldlog.150418-010411
Sat Apr 18 01:59:33 CST 2015 /ouc_lustre/cesm/test_cesm1_0_4/mycase/run/ccsm.bldlog.150418-010411
 - Locking file env_build.xml
 - Locking file Macros.polaris
 CCSM BUILDEXE SCRIPT HAS FINISHED SUCCESSFULLY--------------------------------------------------------------------
FILE::: /bld/pio/pio.bldlog.150418-010411............
Temp variables: {F90=mpif90} {MPIF90=mpif90}Output Variables: {CC=mpicc} {MPICC=mpicc} {ALLCFLAGS=-g -O2 -DFORTRAN_UNDERSCORE_ -DFORTRANUNDERSCORE -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR} {EXPLICIT_FPP=no} {FPP=cpp} {FPPFLAGS=-P -C -N -traditional} {FC=mpif90} {MPIF90=mpif90}{OPT=} {BIT64=} {REAL8=} {ENDIAN=} {FFLAGS= -I/lustre/inspur/mpi/openmpi-intel/include} {CFLAGS=-g -O2} {F90FLAGS=} {MACHDEFS=-DSYSLINUX -DLINUX -DCPRUNKNOWNCPR} {MPI_INC=-I/lustre/inspur/mpi/openmpi-intel/include} {MPI_LIB=} {MODINC=-I} {INCLUDEPATH=} {AR=ar} {ARFLAGS=cq} {USE_PNETCDF=no} {PNETCDF_PATH=/usr/local/pnetcdf} {USE_NETCDF=yes} {NETCDF_PATH=/lustre/inspur/libs/netcdf-4.1.3-intel} {USE_MCT=no} {USEBOX=yes} {PDEFS= -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX} {PDEFSF= -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX} {PINCS=-I/lustre/inspur/mpi/openmpi-intel/include -I/lustre/inspur/libs/netcdf-4.1.3-intel/include} {LDLIBS= -L/lustre/inspur/libs/netcdf-4.1.3-intel/lib -lnetcdf } {DEBUG=no}configure: creating ./config.status
config.status: creating Makefile.conf
Please check the Makefile.conf
Have a nice day!
gmake: warning:  Clock skew detected.  Your build may be incomplete.
...........
the following repeat for too many times .....
............
gmake[1]: Entering directory `/ouc_lustre/cesm/test_cesm1_0_4/mycase/bld/pio'
gmake[1]: Warning: File `pio_kinds.d' has modification time 2.2e+03 s in the future
Making dependencies for pio_msg_getput_callbacks.F90 --> pio_msg_getput_callbacks.d
Making dependencies for pio_spmd_utils.F90 --> pio_spmd_utils.d
Making dependencies for piodarray.F90 --> piodarray.d
Making dependencies for iompi_mod.F90 --> iompi_mod.d
Making dependencies for mct_rearrange.F90 --> mct_rearrange.d
Making dependencies for pio_support.F90 --> pio_support.d
Making dependencies for rearrange.F90 --> rearrange.d
Making dependencies for box_rearrange.F90 --> box_rearrange.d
Making dependencies for alloc_mod.F90 --> alloc_mod.d
Making dependencies for pionfget_mod.F90 --> pionfget_mod.d
Making dependencies for pionfput_mod.F90 --> pionfput_mod.d
Making dependencies for pionfwrite_mod.F90 --> pionfwrite_mod.d
Making dependencies for pionfread_mod.F90 --> pionfread_mod.d
Making dependencies for pionfatt_mod.F90 --> pionfatt_mod.d
gmake[1]: Leaving directory `/ouc_lustre/cesm/test_cesm1_0_4/mycase/bld/pio'
gmake[1]: Entering directory `/ouc_lustre/cesm/test_cesm1_0_4/mycase/bld/pio'
gmake[1]: Warning: File `pio_kinds.d' has modification time 2.2e+03 s in the future
...............................
above content repeat for too many times .....
..............................
gmake[1]: Warning: File `pio_msg_getput_callbacks.F90' has modification time 0.19 s in the future
Making dependencies for pio_msg_getput_callbacks.F90 --> pio_msg_getput_callbacks.d
mpicc -c -g -O2 -DFORTRAN_UNDERSCORE_ -DFORTRANUNDERSCORE -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX  -I/lustre/inspur/mpi/openmpi-intel/include -I/lustre/inspur/libs/netcdf-4.1.3-intel/include topology.c
mpif90 -c -I/lustre/inspur/mpi/openmpi-intel/include  -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -I/lustre/inspur/mpi/openmpi-intel/include -I/lustre/inspur/libs/netcdf-4.1.3-intel/include pio_kinds.F90
.......
ar cq libpio.a topology.o pio.o pio_kinds.o nf_mod.o ionf_mod.o pio_types.o piolib_mod.o pio_mpi_utils.o pio_nf_utils.o pio_utils.o pio_quicksort.o pio_msg_mod.o pio_msg_callbacks.o calcdecomp.o calcdisplace_mod.o pionfatt_mod.o pionfread_mod.o pionfwrite_mod.o pionfput_mod.o pionfget_mod.o alloc_mod.o box_rearrange.o rearrange.o pio_support.o mct_rearrange.o iompi_mod.o piodarray.o pio_spmd_utils.o pio_msg_getput_callbacks.o
gmake[1]: warning:  Clock skew detected.  Your build may be incomplete.
gmake[1]: Leaving directory `/ouc_lustre/cesm/test_cesm1_0_4/mycase/bld/pio'###END
 
S

santos

Member
Note this line:"Warning: File `pio_kinds.d' has modification time 2.2e+03 s in the future"Also:"gmake[1]: warning:  Clock skew detected.  Your build may be incomplete."It seems that there was a problem with the clock on your system. It may be that you had two machines writing to the same file, and one had an inaccurate clock. Or maybe you have one machine, but the system time was corrected (by about 37 minutes) in the middle of the build.This is not a problem with PIO specifically. All build systems that use a Makefile require a consistent system clock.
 
S

santos

Member
Note this line:"Warning: File `pio_kinds.d' has modification time 2.2e+03 s in the future"Also:"gmake[1]: warning:  Clock skew detected.  Your build may be incomplete."It seems that there was a problem with the clock on your system. It may be that you had two machines writing to the same file, and one had an inaccurate clock. Or maybe you have one machine, but the system time was corrected (by about 37 minutes) in the middle of the build.This is not a problem with PIO specifically. All build systems that use a Makefile require a consistent system clock.
 
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