Re: Trouble passing array to f90 subroutine using WRAPIT

From: Mary Haley <haley_at_nyahnyahspammersnyahnyah>
Date: Tue Aug 27 2013 - 16:12:19 MDT

David,

I was using a newer gcc and gfortran, V4.5.0. which is installed in /usr/local/bin on my machine.

I edited WRAPIT to force it to use /usr/bin/gcc, but given that my gfortran is still the 4.5.0 one, I'm not sure if this is a fair test.

Note that I have to use the "-m64", because the MacOS binary was built using the "-m64" option for both gcc and gfortran.

Here's the output with -d, using my modified WRAPIT:

% ./WRAPIT -m64 -d writearr2.f90 writearr2.stub
 
WRAPIT Version: 120209
OPERATING SYSTEM: Darwin
FORTRAN COMPILER (f90c): gfortran
FORTRAN COMPILER OPTIONS (fopts): -m64 -fPIC -v -c -fno-second-underscore
/usr/bin/gcc -m64 -c -fno-common -I/Users/haley/dev/6.1.2/include WRAPIT.c
COMPILING writearr2.f90
gfortran -m64 -fPIC -v -c -fno-second-underscore writearr2.f90
Using built-in specs.
Target: x86_64-apple-darwin10
Configured with: ../gcc-4.5-20090910/configure --enable-languages=fortran,c++ --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10
Thread model: posix
gcc version 4.5.0 20090910 (experimental) (GCC)
COLLECT_GCC_OPTIONS='-mmacosx-version-min=10.6' '-m64' '-fPIC' '-v' '-c' '-fno-second-underscore' '-mtune=generic'
 /usr/local/gfortran-4.5/bin/../libexec/gcc/x86_64-apple-darwin10/4.5.0/f951 writearr2.f90 -fPIC -quiet -dumpbase writearr2.f90 -mmacosx-version-min=10.6 -m64 -mtune=generic -auxbase writearr2 -version -fPIC -fno-second-underscore -fintrinsic-modules-path /usr/local/gfortran-4.5/bin/../lib/gcc/x86_64-apple-darwin10/4.5.0/finclude -o /var/folders/9z/124fjm895y100zbw_00f3mvs7w48jt/T//ccW35pLy.s
GNU Fortran (GCC) version 4.5.0 20090910 (experimental) (x86_64-apple-darwin10)
        compiled by GNU C version 4.5.0 20090910 (experimental), GMP version 4.3.1, MPFR version 2.4.1, MPC version 0.7
GGC heuristics: --param ggc-min-expand=30 --param ggc-min-heapsize=4096
GNU Fortran (GCC) version 4.5.0 20090910 (experimental) (x86_64-apple-darwin10)
        compiled by GNU C version 4.5.0 20090910 (experimental), GMP version 4.3.1, MPFR version 2.4.1, MPC version 0.7
GGC heuristics: --param ggc-min-expand=30 --param ggc-min-heapsize=4096
COLLECT_GCC_OPTIONS='-mmacosx-version-min=10.6' '-m64' '-fPIC' '-v' '-c' '-fno-second-underscore' '-mtune=generic'
 as -arch x86_64 -force_cpusubtype_ALL -o writearr2.o /var/folders/9z/124fjm895y100zbw_00f3mvs7w48jt/T//ccW35pLy.s
COMPILER_PATH=/usr/local/gfortran-4.5/bin/../libexec/gcc/x86_64-apple-darwin10/4.5.0/:/usr/local/gfortran-4.5/bin/../libexec/gcc/
LIBRARY_PATH=/usr/local/gfortran-4.5/bin/../lib/gcc/x86_64-apple-darwin10/4.5.0/:/usr/local/gfortran-4.5/bin/../lib/gcc/:/usr/local/gfortran-4.5/bin/../lib/gcc/x86_64-apple-darwin10/4.5.0/../../../:/usr/lib/
COLLECT_GCC_OPTIONS='-mmacosx-version-min=10.6' '-m64' '-fPIC' '-v' '-c' '-fno-second-underscore' '-mtune=generic'
COLLECT_GCC_OPTIONS='-mmacosx-version-min=10.6' '-m64' '-fPIC' '-v' '-c' '-fno-second-underscore' '-mtune=generic'
SHARED OBJECT NAME (SharedObj): writearr2.so
LINKER SUFFIX (ld_suffix): WRAPIT.o writearr2.o -o writearr2.so
 
LINKING
/usr/bin/gcc -m64 -bundle -flat_namespace -undefined suppress WRAPIT.o writearr2.o -o writearr2.so -lgfortran
END WRAPIT
 
ellabell[548] ncl writearr2.ncl
 Copyright (C) 1995-2013 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.1.2
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0) xtas(0,0) in NCL: 0.323711
 0.324

On Aug 27, 2013, at 3:33 PM, David Rasmussen wrote:

> This may be more of a system related issue. What version of xcode and/or gcc is Mary using? Can she do a WRAPIT -d? I am running gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
>
>
> On Tue, Aug 27, 2013 at 3:50 PM, Rick Brownrigg <brownrig@ucar.edu> wrote:
> Hi David,
>
> This issue is quite perplexing, as my colleague Mary Haley is able to run the code you sent yesterday just fine on her Mac, on all 6.x.x versions of NCL. I don't have anything but the current code trunk (i.e., 6.2.0) available to test in my Mac.
>
> In any case, perhaps the attached binary will work for you? Let me know if notů
>
> Rick
>
>
> On Aug 27, 2013, at 11:56 AM, David Rasmussen <drasmussen@ucdavis.edu> wrote:
>
>> 'fbinrecwrite' will be useful for future applications. The current task deals with several records, so a faster method (i.e. fortran) is needed.
>>
>>
>>
>> On Tue, Aug 27, 2013 at 9:42 AM, Dennis Shea <shea@ucar.edu> wrote:
>> Of course, if it was just 'xtas' or 'itas' ... you could
>> use 'fbinrecwrite'
>>
>> fbin = "foo.bin" ; ".bin" is not needed
>>
>> head = (/ year,month, day, hour/) ; header record
>>
>> fbinrecwrite(fbin, -1, head) ; header
>> fbinrecwrite(fbin, -1, xtas) ; float
>> fbinrecwrite(fbin, -1, itas) ; integer
>>
>> The issue with NCL's fbinrecwrite are:
>> (1) it only allows one variable/type.
>> Unlike fortran which allows multiple variable
>> of mixed type: write(...) head, xtas, itas
>>
>> (2) when there are *many* records being written it can
>> become slow.
>>
>> http://www.ncl.ucar.edu/Document/Functions/Built-in/fbinrecwrite.shtml
>>
>>
>> On 8/26/13 8:29 PM, brownrig@ucar.edu wrote:
>> David,
>>
>> We can most likely get you a 6.2.0-prerelease; let me get back to you
>> in the morning on that.
>>
>> Rick
>>
>> On Mon, 26 Aug 2013 19:25:40 -0400
>> David Rasmussen <drasmussen@ucdavis.edu> wrote:
>> I am on a mac with the current version of NCL: 6.1.2
>>
>> Like Dennis, I too produce the error with the current version:
>>
>> (0) xtas(1,1) in NCL: 0.387302
>> At line 6 of file writearr2.f90 (unit = 6, file = 'stdout')
>> Internal Error: list_formatted_write(): Bad type
>>
>> Both Rick and Dennis had success running the code with NCL 6.2.0 on
>> a Mac.
>> Are binaries of NCL 6.2.0 for OS X available as beta software at
>> this time?
>>
>>
>>
>> On Mon, Aug 26, 2013 at 5:19 PM, Dennis Shea <shea@ucar.edu> wrote:
>>
>> To my knowledge, there has been nothing explicitly
>> done with NCL's WRAPIT in a *long* time.
>>
>> I used the following and added one extra print [write(*/6,...) ]:
>>
>>
>> subroutine writearr(ntim,nmod,xtas)
>> implicit none
>> integer, intent(in) ::ntim,nmod
>> real, intent(in) ::xtas(ntim,nmod)
>>
>> print*,"f90: xtas(1,1)=", xtas(1,1)
>>
>> write(*,'(f6.3)') xtas(1,1) <==== or write(6,....)
>> return
>> end subroutine writearr
>>
>>
>> ****ON MY MAC****, the , as yet unreleased NCL v6.2.0 works
>> perfectly !
>>
>> %> ncl write.ncl_so
>>
>> Copyright (C) 1995-2013 - All Rights Reserved
>>
>> University Corporation for Atmospheric Research
>> NCAR Command Language Version 6.2.0-23Aug2013_0133 <========
>>
>> The use of this software is governed by a License Agreement.
>> See http://www.ncl.ucar.edu/ for more details.
>> (0) xtas(1,1) in NCL: 0.387302
>> f90: xtas(1,1)= 0.323710531
>> 0.324
>> =================
>>
>> However, ****ON MY MAC****, with the current version of NCL: 6.1.2
>>
>> %> ncl write.ncl_so
>>
>> Copyright (C) 1995-2013 - All Rights Reserved
>>
>> University Corporation for Atmospheric Research
>> NCAR Command Language Version 6.1.2
>>
>> The use of this software is governed by a License Agreement.
>> See http://www.ncl.ucar.edu/ for more details.
>>
>> (0) xtas(1,1) in NCL: 0.387302
>> At line 6 of file writearr2.f90 (unit = 6, file = 'stdout')
>> Internal Error: list_formatted_write(): Bad type
>>
>> *************************************************************
>>
>> However, on 2 independent linux systems (local divisional
>> computers and on the yellowstone complex) the code
>> works just fine with 6.1.2
>>
>> D
>>
>>
>>
>>
>> On 8/26/13 1:43 PM, David Rasmussen wrote:
>>
>> I forgot to mention that when I tried passing a 2-D integer array, I
>> re-declared all relevant variables as integers.
>>
>> What I found is that using...
>>
>> C NCLFORTSTART
>> subroutine writeint(ntim,nmod,xtas)
>> implicit none
>> integer ntim,nmod
>> integer xtas(nmod,ntim)
>> C NCLEND
>>
>> ...works as expected. When I re-declare all relevant variables as
>> floats/reals and use the following...
>>
>>
>> C NCLFORTSTART
>> subroutine writeflt(ntim,nmod,xtas)
>> implicit none
>>
>> integer ntim,nmod
>> real xtas(nmod,ntim)
>> C NCLEND
>>
>> ...I get the error:
>>
>> Line: 32 write(6,'(f6.3)') xtas(1,1)
>>
>> At line 32 of file writearr.f90 (unit = 6, file = 'stdout')
>> Fortran runtime error: Expected REAL for item 2 in formatted
>> transfer, got
>> CHARACTER
>> (f6.3)
>>
>> ...when I print xtas(1,1) unformatted (i.e. using print*), I get
>> "????" (4
>> question marks).
>>
>> I am also changing data types & format codes in my .f90 and data
>> types in
>> my .ncl file in between these tests. Everything compiles without
>> error.
>>
>> There seems to be an issue passing float/reals. I also tried passing
>> double
>> precision and the same result occurred. I am not sure why I am
>> experiencing
>> this behavior.
>>
>>
>> On Mon, Aug 26, 2013 at 3:22 PM, Dennis Shea <shea@ucar.edu> wrote:
>>
>> Below you created
>>
>>
>> C NCLFORTSTART
>> subroutine writearr(ntim,nmod,xtas)
>> integer ntim,nmod
>> real xtas(nmod,ntim)
>> C NCLEND
>>
>>
>> which declares 'xtas' as type 'real' (ie, a float)
>>
>> If you passed integers in 'xtas', there would be a problem.
>> However, passing variables of type float/real should be
>> exactly what is expected. Just the opposite of what you
>> stated below. One approach to writing floats and
>> integers is:
>>
>>
>>
>> C NCLFORTSTART
>> subroutine writeint(ntim,nmod,xtas)
>> implicit none
>> integer ntim,nmod
>> integer xtas(nmod,ntim)
>> C NCLEND
>>
>>
>>
>>
>> On 8/26/13 12:55 PM, David Rasmussen wrote:
>>
>> I take back some of what I said. The problem seems to be dependent
>> on
>> the
>> variable type. I can pass 2-D integer arrays just fine, but I have
>> trouble
>> with floats, which is what I would like to pass between NCL and my
>> f90
>> subroutine.
>>
>>
>> On Mon, Aug 26, 2013 at 1:34 PM, David Rasmussen <
>> drasmussen@ucdavis.edu
>>
>> wrote:
>>
>>
>> No errors now, but when I print elements of the array I just get 4
>>
>> question marks (i.e "????") (I am guessing one for each byte?)
>>
>> When I try and format the output, Fortran tells me that my format
>> choice
>> is invalid because the data is of type character....
>>
>> Line: 32 write(6,'(f6.3)') xtas(1,1)
>>
>> At line 32 of file writearr.f90 (unit = 6, file = 'stdout')
>> Fortran runtime error: Expected REAL for item 2 in formatted
>> transfer,
>> got
>> CHARACTER
>> (f6.3)
>>
>> I am able to print results from passed 1-D arrays OK. For passing
>> 2-D
>> arrays, does anything else special need to happen besides swapping
>> array
>> dimensions in the stub file? Again, my subroutine is f90.
>>
>> Thanks!
>>
>>
>> On Mon, Aug 26, 2013 at 11:07 AM, Dennis Shea <shea@ucar.edu> wrote:
>>
>> Computer rule: Fastest varying dimension maps into fastest
>>
>> varying dimension. NCL (row major like C) is 0 based and the
>> rightmost dimension varies fastest. Fortran is column major
>> and the leftmost dimension varies fastest.
>>
>> Dimension order and subscripting are different for different
>> languages.
>>
>> NCL: x(NA,NB,NC) <===> x(NC,NC,NA) : fortran
>>
>> In computer memory, think of the arrays as a long linear list and
>> the
>> elements are accessed via a particular language's conventions
>>
>> See: page 37: http://www.ncl.ucar.edu/****
>> Document/Manuals/language_man.******<http://www.ncl.ucar.edu/***
>> *Document/Manuals/language_**man.**<http://www.ncl.ucar.edu/**Document/Manuals/language_man.**>
>>
>> pdf <http://www.ncl.ucar.edu/****Document/Manuals/language_man.**
>> **pdf
>> <http://www.ncl.ucar.edu/**Document/Manuals/language_man.**pdf>
>> <http://www.ncl.ucar.edu/**Document/Manuals/language_man.**pdf<http://www.ncl.ucar.edu/Document/Manuals/language_man.pdf>
>>
>>
>>
>>
>>
>> ---
>> It should be:
>>
>>
>> C NCLFORTSTART
>> subroutine writearr(ntim,nmod,xtas)
>> integer ntim,nmod
>> real xtas(nmod,ntim)
>> C NCLEND
>>
>> Note:No data rearranging should be done.
>>
>>
>>
>> On 8/26/13 8:47 AM, David Rasmussen wrote:
>>
>> Hi,
>>
>>
>> I would like to write an array of data to a text file, similar to
>> this
>> request from a previous thread:
>> http://www.ncl.ucar.edu/******Support/talk_archives/2012/*****
>> *0230.html<http://www.ncl.ucar.edu/****Support/talk_archives/2012/****0230.html>
>> <http://www.ncl.**ucar.edu/**Support/talk_**
>> archives/2012/**0230.html<http://www.ncl.ucar.edu/**Support/talk_archives/2012/**0230.html>
>>
>> <http://www.ncl.ucar.**edu/**Support/talk_archives/**2012/**
>> 0230.html<http://www.ncl.ucar.**edu/Support/talk_archives/**
>> 2012/0230.html<http://www.ncl.ucar.edu/Support/talk_archives/2012/0230.html>
>>
>>
>>
>>
>>
>> I have chosen to use WRAPIT to write my data to disk.
>>
>> I am trying to pass an array to an f90 subroutine, but NCL/WRAPIT
>> keeps
>> telling me that my array is not dimensioned correctly.
>>
>> I have an array defined in the driving NCL script as:
>>
>> xtas(ntim,nmod), where ntim=34675, nmod=33
>>
>> I would like to pass this array to a f90 routine. When I try and do
>> this,
>> the routine expects xtas to be dimensioned xtas(nmod,ntim) which is
>> NOT
>> how
>> it is defined in the driving NCL script...
>>
>> fatal:writearr: dimension size of dimension (1) of xtas must be
>> equal
>> to
>> the value of ntim
>> fatal:["Execute.c":8128]:******Execute: Error occurred at or near
>> line
>>
>> 226
>>
>> in
>> file extract_BCSD_lat_lon.ncl
>>
>> The call to the routine in the NCL script is:
>> WRITEARRAY::writearr(ntim,******nmod,xtas)
>>
>>
>>
>> Immediately before calling the f90 routine, I do
>> "printVarSummary(xtas)"...
>>
>> I get...
>>
>> Variable: xtas
>> Type: float
>> Total Size: 4577100 bytes
>> 1144275 values
>> Number of Dimensions: 2
>> Dimensions and sizes: [34675] x [33]
>> Coordinates:
>> Number Of Attributes: 1
>> _FillValue : -999.999
>>
>> The print summary for xtas is as expected...xtas(ntim,nmod)...
>>
>> my stub file is:
>>
>> C NCLFORTSTART
>> subroutine writearr(ntim,nmod,xtas)
>> integer ntim,nmod
>> real xtas(ntim,nmod)
>> C NCLEND
>>
>> my f90 routine is:
>>
>> subroutine writearr(ntim,nmod,xtas)
>> integer ntim, nmod
>> real xtas(ntim,nmod)
>>
>> print*, xtas
>>
>> return
>> end subroutine writearr
>>
>> Both compile with no errors.
>>
>> Other info:
>>
>> WRAPIT Version: 120209
>> OPERATING SYSTEM: Darwin
>> FORTRAN COMPILER (f90c): gfortran
>> FORTRAN COMPILER OPTIONS (fopts): -m64 -fPIC -v -c
>> -fno-second-underscore
>> gcc -m64 -c -fno-common -I/usr/local/ncl-6.1.2/include WRAPIT.c
>> COMPILING writearr.f90
>> gfortran -m64 -fPIC -v -c -fno-second-underscore writearr.f90
>> Using built-in specs.
>> COLLECT_GCC=gfortran
>> COLLECT_LTO_WRAPPER=/usr/******local/gfortran/libexec/gcc/**
>> x86_64-apple-darwin11/4.6.2/******lto-wrapper
>> Target: x86_64-apple-darwin11
>> Configured with: ../gcc-4.6.2-RC-20111019/******configure
>> --prefix=/usr/local/gfortran
>> --with-gmp=/Users/fx/devel/******gcc/deps-static/x86_64
>> --enable-languages=c,c++,******fortran,objc,obj-c++
>>
>>
>> --build=x86_64-apple-darwin11
>> Thread model: posix
>> gcc version 4.6.2 20111019 (prerelease) (GCC)
>> COLLECT_GCC_OPTIONS='-mmacosx-******version-min=10.8.3' '-m64'
>> '-fPIC'
>> '-v'
>> '-c'
>> '-fno-second-underscore' '-mtune=core2'
>> /usr/local/gfortran/libexec/******gcc/x86_64-apple-darwin11/4.**
>> 6.**
>>
>> **2/f951
>>
>> writearr.f90 -fPIC -quiet -dumpbase writearr.f90
>> -mmacosx-version-min=10.8.3 -m64 -mtune=core2 -auxbase writearr
>> -version
>> -fPIC -fno-second-underscore -fintrinsic-modules-path
>> /usr/local/gfortran/lib/gcc/******x86_64-apple-darwin11/4.6.2/**
>> ****finclude
>> -o
>> /var/folders/fl/******p8bxmn6x0gb7vk2qlzv90bdh0000gn**
>> ****/T//cc8VXUoN.s
>>
>>
>> GNU Fortran (GCC) version 4.6.2 20111019 (prerelease)
>> (x86_64-apple-darwin11)
>> compiled by GNU C version 4.6.2 20111019 (prerelease), GMP version
>> 5.0.2,
>> MPFR version 3.0.1-p4, MPC version 0.9
>> GGC heuristics: --param ggc-min-expand=100 --param
>> ggc-min-heapsize=131072
>> GNU Fortran (GCC) version 4.6.2 20111019 (prerelease)
>> (x86_64-apple-darwin11)
>> compiled by GNU C version 4.6.2 20111019 (prerelease), GMP version
>> 5.0.2,
>> MPFR version 3.0.1-p4, MPC version 0.9
>> GGC heuristics: --param ggc-min-expand=100 --param
>> ggc-min-heapsize=131072
>> COLLECT_GCC_OPTIONS='-mmacosx-******version-min=10.8.3' '-m64'
>> '-fPIC'
>>
>> '-v'
>>
>> '-c'
>> '-fno-second-underscore' '-mtune=core2'
>> as -arch x86_64 -force_cpusubtype_ALL -o writearr.o
>> /var/folders/fl/******p8bxmn6x0gb7vk2qlzv90bdh0000gn**
>> ****/T//cc8VXUoN.s
>> COMPILER_PATH=/usr/local/******gfortran/libexec/gcc/x86_64-**
>> apple-darwin11/4.6.2/:/usr/******local/gfortran/libexec/gcc/**
>> x86_64-apple-darwin11/4.6.2/:/******usr/local/gfortran/**
>> libexec/****
>> gcc/x86_64-apple-darwin11/:/******usr/local/gfortran/lib/gcc/****
>> x86_64-apple-darwin11/4.6.2/:/******usr/local/gfortran/lib/**
>> gcc/****
>> x86_64-apple-darwin11/
>> LIBRARY_PATH=/usr/local/******gfortran/lib/gcc/x86_64-apple-******
>> darwin11/4.6.2/:/usr/local/******gfortran/lib/gcc/x86_64-**
>> apple-****
>> darwin11/4.6.2/../../../:/usr/******lib/
>> COLLECT_GCC_OPTIONS='-mmacosx-******version-min=10.8.3' '-m64'
>> '-fPIC'
>>
>> '-v'
>>
>> '-c'
>> '-fno-second-underscore' '-mtune=core2'
>> SHARED OBJECT NAME (SharedObj): writearr2.so
>> LINKER SUFFIX (ld_suffix): WRAPIT.o writearr.o
>> -L/usr/local/gfortran/lib/
>> -o writearr2.so
>>
>> LINKING
>> gcc -m64 -bundle -flat_namespace -undefined suppress WRAPIT.o
>> writearr.o
>> -L/usr/local/gfortran/lib/ -o writearr2.so -lgfortran
>> END WRAPIT
>>
>> I must be missing something here. I am not trying to do anything
>> complicated. Thanks in advance.
>>
>>
>>
>> ______________________________******_________________
>>
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>>
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Received on Tue Aug 27 16:12:33 2013

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