{"id":2687,"date":"2019-11-21T19:59:53","date_gmt":"2019-11-21T10:59:53","guid":{"rendered":"http:\/\/home.hiroshima-u.ac.jp\/~leehs\/?p=2687"},"modified":"2019-11-22T18:55:11","modified_gmt":"2019-11-22T09:55:11","slug":"how-to-compile-fvcom4-3-series-mode","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/?p=2687","title":{"rendered":"How to compile FVCOM4.3 (Series mode)"},"content":{"rendered":"\n

This is a technical note on how to build and execute FVCOM 4.3 in series mode using Intel compilers on CHESS lab HPC at Hiroshima University. Suppose the source code exists in\u00a0fvcom43\/FVCOM_source<\/code>, and\u00a0fvcom43\/Examples\/River plume<\/code>\u00a0is a selected test case. <\/p>\n\n\n\n

Check line feed of source files<\/h4>\n\n\n\n

Some line feed in the source files was CRLF<\/code> (this is for Windows while LF for Linux). Check them using the file<\/code> command and convert them to LF<\/code> using dos2unix<\/code>.<\/p>\n\n\n\n

$ <\/em>file *.F<\/pre>\n\n\n\n
If displayed as ASCII text<\/code> with  CRLF line terminators, convert the file using  dos2unix<\/code> command <\/p>\n\n\n\n
$ dos2unix *.F <\/pre>\n\n\n\n
Preparing libraries<\/h4>\n\n\n\n
Before compiling FVCOM, you need to prepare the necessary libraries in .\/FVCOM_source\/libs<\/code>. netCDF should be installed separately (see here<\/a>). In .\/FVCOM_source<\/code>, copy make.inc_example<\/code> to make.inc<\/code> and edit it.$ <\/em>cp make.inc_example make.inc<\/p>\n\n\n\n
First, set TOPDIR<\/code> as follows:           <\/p>\n\n\n\n
TOPDIR = \/home2\/hslee\/FVCOM\/fvcom43\/FVCOM_source<\/pre>\n\n\n\n
Next, set the path of the libraries. Comment out its part of MEDM ENVIRONMENT and set LOCAL INSTALL as follows. Also, activate DTLIBS and DTINCS.<\/p>\n\n\n\n
####################### MEDM ENVIRONMENT #################################<\/em>\n# Use the environmental variables, LIBPATH and INCLUDEPATH, set by MODULE<\/em>\n# to find the packages used by this build.<\/em>\n# colon =:<\/em>\n# empty =<\/em>\n# dashI = $(empty) - I<\/em>\n# dashL = $(empty) - L<\/em>\n# ### UNCOMMENT HERE!<\/em>\n# LIBDIR = -L (subst(subst(colon), (dashL),(dashL),(LIBPATH))<\/em>\n# INCDIR = -I (subst(subst(colon), (dashI),(dashI),(INCLUDEPATH))<\/em><\/pre>\n\n\n\n
###########################################################################<\/em><\/pre>\n\n\n\n
# LOCAL INSTAL<\/em>\n             LIBDIR = -L$(INSTALLDIR)\/lib\n             INCDIR = -I$(INSTALLDIR)\/include\n# ------------------------------------------------------------------------<\/em>\n# STANDARD LIBRARIES FOR DATA AND TIME IN fVCOM:<\/em>\n#<\/em>\n             DTLIBS = -ljulian\n             DTINCS =\n#            DTLIBS = -L\/${TOPDIR}\/libs<\/em>\n#            DTINCS =<\/em><\/pre>\n\n\n\n
 Next, set the environment variable for Intel compilers in series. Optimization is to stay at -O3 at this moment. <\/p>\n\n\n\n
 # -----------------------------------------------------------------------<\/em>\n# Intel Compiler Definitions for Series<\/em>\n# ------------------------------------------------------------------------<\/em>\n         CPP      = \/usr\/bin\/cpp\n         COMPILER = -DIFORT\n         FC       = ifort\n         CC       = icc\n         CXX      = icpc\n         CFLAGS = -O3\n         DEBFLGS = # -check all<\/em>\n         OPT = -O3 <\/pre>\n\n\n\n
 Next, move to .\/FVCOM_source\/libs<\/code>, and open and edit makefile<\/code>: <\/p>\n\n\n\n
PACKAGES = proj fproj julian<\/pre>\n\n\n\n
Delete metis<\/code> and netcdf<\/code>. Similarly, comment out the parts associated with metis<\/code> and netcdf<\/code> below. metis<\/code> should be installed when executing in MPI<\/code>. Then execute make<\/code>:<\/p>\n\n\n\n
$ <\/em>make<\/pre>\n\n\n\n
.\/install<\/code> These libraries should have been installed in directories below .\/install<\/code>.<\/p>\n\n\n\n
Edit make.inc<\/h4>\n\n\n\n
Return to .\/FVCOM_source<\/code> directory, open make.inc<\/code>, confirm the Intel compiler environment parameters are defined and the full path to FVCOM_source<\/code> is set at TOPDIR<\/code>. In addition, set the environmental parameters for netcdf<\/code>:<\/p>\n\n\n\n
### netcdf (CHESS lab HPC)\nIOLIBS = -L\/usr\/local\/netcdf-3.6.3_intel\/lib -lnetcdf\nIOINCS = -I\/usr\/local\/netcdf-3.6.3_intel\/include<\/pre>\n\n\n\n
Next,\u00a0FLAG<\/code>\u00a0should be edited according to the simulation condition. Here, as an example of\u00a0Examples\/River plume<\/code>,\u00a0FLAGs<\/code>\u00a0to be activated are shown below:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/p>\n\n\n\n
FLAG_1 =  -DDOUBLE_PRECISION
FLAG_3 =  -DWET_DRY
FLAG_8 =  -DLIMITED_NO
FLAG_10 = -DGCN
FLAG_14 = -DRIVER_FLOAT<\/pre>\n\n\n\n
Correct typo in makefile<\/h4>\n\n\n\n
The module of\u00a0mod_esmf_nesting.F<\/code>\u00a0is not in\u00a0use<\/code>\u00a0anywhere, and thus it seems that it is not used. To avoid linking error, delete\u00a0mod_esmf_nesting.F<\/code>\u00a0in\u00a0makefile<\/code>.<\/p>\n\n\n\n
Edit the makedepends<\/h4>\n\n\n\n
Remove the line for mod_esmf_nesting.F<\/code> in the makedepends<\/code> file.<\/p>\n\n\n\n
Or, you can recreate the makedepends<\/code> file as below. But it takes a long time in a case.<\/p>\n\n\n\n
Recreate makedepends<\/h4>\n\n\n\n
The file of makedepends<\/code> needs to be recreated using makedepf90<\/code> (unless installed, see here) in the directory of .\/FVCOM_source<\/code> as follows:<\/p>\n\n\n\n
$ rm makedepneds
$ touch makedepends
$ make depend<\/pre>\n\n\n\n
Minor correction of a source file (for FVCOM4.1)<\/h4>\n\n\n\n
To avoid Warning<\/code> at compile time, delete the comment below at line 131 in wreal.F<\/code>.<\/p>\n\n\n\n
#\u00a0<\/em>endif\u00a0!!\u00a0ice_embedding yding<\/pre>\n\n\n\n
In FVCOM4.3, the line 131 is modified already so that it does not need to edit in wreal.F<\/code>.<\/p>\n\n\n\n
Build FVCOM4.3<\/h4>\n\n\n\n
Now you can build FVCOM4.3<\/code> in .\/FVCOM_source<\/code>:<\/p>\n\n\n\n
$ make<\/pre>\n\n\n\n
Successful if the executable file of fvcom<\/code> is created.<\/p>\n\n\n\n
Interactive execution of test case River Plume<\/h4>\n\n\n\n
Run a basic test case of\u00a0River Plume<\/code>\u00a0interactively. The file of\u00a0chn_run.nml<\/code>\u00a0of\u00a0River plume<\/code>\u00a0has a bug. Move to\u00a0..\/Examples\/River Plume\/run<\/code>\u00a0and open\u00a0chn_run.nml<\/code>\u00a0with an editor and change the number of rivers to\u00a00<\/code>\u00a0(the original was 3).<\/p>\n\n\n\n
& NML_RIVER_TYPE\nRIVER_NUMBER = 1,<\/pre>\n\n\n\n
Add the NML_NETCDF_SURFACE section in the chn_run.nml<\/code>.<\/p>\n\n\n\n
&NML_NETCDF_SURFACE\n NCSF_ON = F,\n NCSF_FIRST_OUT  = 'seconds=0.0'   ,\n NCSF_OUT_INTERVAL       = 'second=3600.'  ,\n NCSF_OUTPUT_STACK       =           0,\n NCSF_SUBDOMAIN_FILES    = FVCOM,\n NCSF_GRID_METRICS       = F,\n NCSF_FILE_DATE  = F,\n NCSF_VELOCITY   = F,\n NCSF_SALT_TEMP  = F,\n NCSF_TURBULENCE = F,\n NCSF_WIND_VEL   = F,\n NCSF_WIND_STRESS        = F,\n NCSF_EVAP_PRECIP        = F,\n NCSF_SURFACE_HEAT       = F\n \/<\/pre>\n\n\n\n
Copy the executable file of\u00a0fvcom<\/code>\u00a0created in\u00a0.\/fvcom43\/FVCOM_source\/<\/code>\u00a0to the current directory (.\/fvcom43\/Examples\/River plume\/run<\/code>\u00a0(or set up the link)) and execute:<\/p>\n\n\n\n
$\u00a0<\/em>.\/fvcom\u00a0--casename=chn<\/pre>\n\n\n\n
Progress of computation is displayed on the screen, and when completed,\u00a0TADA!<\/code>\u00a0should be displayed at the end. Also,\u00a0chn_0001.nc<\/code>\u00a0containing the calculation result should have been created.<\/p>\n","protected":false},"excerpt":{"rendered":"
This is a technical note on how to build and execute FVCOM 4.3 in series mode using Intel compilers on CHESS lab HPC at Hiroshima University. Suppose the source code exists in\u00a0fvcom43\/FVCOM_source, and\u00a0fvcom43\/Examples\/River plume\u00a0is a selected test case. Check line…
Read more<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[12],"tags":[],"class_list":["post-2687","post","type-post","status-publish","format-standard","hentry","category-tool"],"rttpg_featured_image_url":null,"rttpg_author":{"display_name":"hslee","author_link":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/?author=1"},"rttpg_comment":0,"rttpg_category":"Tool<\/a>","rttpg_excerpt":"This is a technical note on how to build and execute FVCOM 4.3 in series mode using Intel compilers on CHESS lab HPC at Hiroshima University. Suppose the source code exists in\u00a0fvcom43\/FVCOM_source, and\u00a0fvcom43\/Examples\/River plume\u00a0is a selected test case. Check line...Read more","_links":{"self":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/posts\/2687","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2687"}],"version-history":[{"count":13,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/posts\/2687\/revisions"}],"predecessor-version":[{"id":2717,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/posts\/2687\/revisions\/2717"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2687"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2687"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2687"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}