[MITgcm-support] Re-a problem in compiling MITgcm using intel compiler (Yu Zhang)
Yu Zhang
yusophie.zhang at gmail.com
Thu Apr 2 22:31:31 EDT 2015
Dear All,
I looked the genmake.log file and found the following error message:
icc -O0 -ip -m64 -xHost -mcmodel=medium -c genmake_tc_1.c
Catastrophic error: could not set locale "" to allow processing of
multibyte characters
After googling online, I tried to add the following two lines in my
.bash_profile :
export LANG=en_US.UTF-8
export LC_ALL=en_US
Now the problem seems to be solved and the test case can be run, but I am
still not quite sure whether this is proper or not. What do you think?
Besides, I got the following warning in the file:
/lustre/intel/Compiler/11.1/072/lib/intel64/libimf.so: warning: warning:
feupdateenv is not implemented and will always fail
Do you know whether this is a serious issue and what I can do about it?
Thanks a lot.
Best,
Yu (Sophie) Zhang
Key laboratory of Physical Oceanography (POL)
Ocean University of China
Office phone number: 011-86-532-82032071
On Fri, Apr 3, 2015 at 12:00 AM, <mitgcm-support-request at mitgcm.org> wrote:
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> Today's Topics:
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> 1. a problem in compiling MITgcm using intel compiler (Yu Zhang)
> 2. Free exchange across OBC (Neil Fraser)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 2 Apr 2015 17:26:17 +0800
> From: Yu Zhang <yusophie.zhang at gmail.com>
> To: mitgcm-support at mitgcm.org
> Subject: [MITgcm-support] a problem in compiling MITgcm using intel
> compiler
> Message-ID:
> <CA+GBDUqgCdpNEYYOsoV+e+8UpCpdOAYY=
> zWhht28BoOcWOBe-w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear All,
>
> I right now have a very weird problem in compiling MITgcm. I am using
> build_option profile linux_amd64_ifort11 with openmpi-intel compiler. The
> message following running genmake command is as follows:
>
> [zhangyu at polaris build]$ /lustre/home/zhangyu/MITgcm/tools/genmake2
> -mods=/lustre/home/zhangyu/MITgcm/verification/front_relax/code -mpi -of
>
> /lustre/home/zhangyu/MITgcm/tools/build_options/linux_amd64_ifort11_polaris_Lu
>
>
> GENMAKE :
>
>
> A program for GENerating MAKEfiles for the MITgcm project.
>
> For a quick list of options, use "genmake2 -h"
>
> or for more detail see the Developer's HOWTO manual at:
>
> http://mitgcm.org/public/docs.html
>
>
> === Processing options files and arguments ===
>
> getting local config information: none found
>
> Warning: ROOTDIR was not specified ; try using a local copy of MITgcm found
> at "../../.."
>
> getting OPTFILE information:
>
> using
>
> OPTFILE="/lustre/home/zhangyu/MITgcm/tools/build_options/linux_amd64_ifort11_polaris_Lu"
>
> getting AD_OPTFILE information:
>
> using AD_OPTFILE="../../../tools/adjoint_options/adjoint_default"
>
> check makedepend (local: 0, system: 0, 0)
>
> Turning on MPI cpp macros
>
>
> === Checking system libraries ===
>
> Do we have the system() command using mpif77... yes
>
> Do we have the fdate() command using mpif77... yes
>
> Do we have the etime() command using mpif77... yes
>
> Can we call simple C routines (here, "cloc()") using mpif77... no
>
> Can we unlimit the stack size using mpif77... no
>
> Can we register a signal handler using mpif77... no
>
> Can we use stat() through C calls... no
>
> Can we create NetCDF-enabled binaries... no
>
> Can we create LAPACK-enabled binaries... no
>
> Can we call FLUSH intrinsic subroutine... yes
>
>
> === Setting defaults ===
>
> Adding MODS directories:
> /lustre/home/zhangyu/MITgcm/verification/front_relax/code
>
> Making source files in eesupp from templates
>
> Making source files in pkg/exch2 from templates
>
> Making source files in pkg/regrid from templates
>
>
> === Determining package settings ===
>
> getting package dependency info from ../../../pkg/pkg_depend
>
> getting package groups info from ../../../pkg/pkg_groups
>
> checking list of packages to compile:
>
> using
>
> PKG_LIST="/lustre/home/zhangyu/MITgcm/verification/front_relax/code/packages.conf"
>
> before group expansion packages are: gfd gmredi diagnostics
>
> replacing "gfd" with: mom_common mom_fluxform mom_vecinv
> generic_advdiff debug mdsio rw monitor
>
> after group expansion packages are: mom_common mom_fluxform mom_vecinv
> generic_advdiff debug mdsio rw monitor gmredi diagnostics
>
> applying DISABLE settings
>
> applying ENABLE settings
>
> packages are: debug diagnostics generic_advdiff gmredi mdsio
> mom_common mom_fluxform mom_vecinv monitor rw
>
> applying package dependency rules
>
> packages are: debug diagnostics generic_advdiff gmredi mdsio
> mom_common mom_fluxform mom_vecinv monitor rw
>
> Adding STANDARDDIRS='eesupp model'
>
> Searching for *OPTIONS.h files in order to warn about the presence
>
> of "#define "-type statements that are no longer allowed:
>
> found CPP_EEOPTIONS="../../../eesupp/inc/CPP_EEOPTIONS.h"
>
> found CPP_OPTIONS="../../../model/inc/CPP_OPTIONS.h"
>
> Creating the list of files for the adjoint compiler.
>
>
> === Creating the Makefile ===
>
> setting INCLUDES
>
> Determining the list of source and include files
>
> Writing makefile: Makefile
>
> Add the source list for AD code generation
>
> Making list of "exceptions" that need ".p" files
>
> Making list of NOOPTFILES
>
> Add rules for links
>
> Adding makedepend marker
>
>
> === Done ===
>
> Interesting thing is I can find mpif77 and mpicc using "which" command.
> What is more interesting is when on a different computer (MAC or windows)
> and logged onto the same account on the same cluster, the genmake step goes
> smoothly without those annoying nos. I have no idea what's wrong here, do
> you guys have any clue? Thanks a lot for your help.
>
> Best regards,
>
>
> Yu (Sophie) Zhang
> Key laboratory of Physical Oceanography (POL)
> Ocean University of China
> Office phone number: 011-86-532-82032071
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> ------------------------------
>
> Message: 2
> Date: Thu, 2 Apr 2015 14:24:45 +0000
> From: Neil Fraser <Neil.Fraser at sams.ac.uk>
> To: "mitgcm-support at mitgcm.org" <mitgcm-support at mitgcm.org>
> Subject: [MITgcm-support] Free exchange across OBC
> Message-ID:
> <4283CB1DAE0FCF47ADEE3EBD2CCEFE2528FAF4DF at Verbiage1.sams.local>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Everyone,
>
> I am running as experiment to study the effects of certain wind events on
> the stratification inside my domain. My domain has 3 open boundaries, with
> the northern edge bounded by coastline.
>
> My problem is this: if I keep the boundary forcing constant (with or
> without the sponge method), the stratification at the boundary is then
> constant in time and affects any changes in the stratification of the
> interior. However, if I prescribe time-varying boundary conditions I must
> assume prior knowledge of how the stratification changes with these wind
> events, which is exactly what I am trying to study.
>
> Is there a configuration allowing free exchange between inside the domain
> and outside? i.e. allow water to advect in and out of the domain, with
> velocities determined by pressure gradients between boundary points and
> adjacent interior points, and with T and S of any inflow matching that of
> the boundary on the previous timestep.
>
> Right now I have Orlanski and Balance turned on, and I am seeing some
> unwanted boundary effects propagating into the domain.
>
> Any help greatly appreciated,
>
> Cheers,
>
> Neil
> The Scottish Association for Marine Science (SAMS) is registered in
> Scotland as a Company Limited by Guarantee (SC009292) and is a registered
> charity (9206). SAMS has two actively trading wholly owned subsidiary
> companies: SAMS Research Services Ltd (SC224404) and SAMS Ltd (SC306912).
> All Companies in the group are registered in Scotland and share a
> registered office at Scottish Marine Institute, Oban Argyll PA37 1QA. The
> content of this message may contain personal views which are not the views
> of SAMS unless specifically stated. Please note that all email traffic is
> monitored for purposes of security and spam filtering. As such individual
> emails may be examined in more detail.
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