real beginer

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real beginer

Trixie
I'm real beginner with cygwin, actually linux and everything related.
But i need to instal and use certain fortran based program. I installed cygwin and several packages. I'm trying to call certain module and all i get is
bash: module: command not found
I googled it up and i found the solution that i should call /etc/profile.d/modules.sh before my module. but there is now module.sh in my /profile.d folder! Did i miss some package to install? What should i do?
Please help! I desperately need to start that program :(((
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Re: real beginer

Earnie Boyd
On Tue, Oct 23, 2012 at 9:28 AM, Trixie <[hidden email]> wrote:
> Please help! I desperately need to start that program :(((

What is the name of the program and where is it located?

> Documentation:         http://cygwin.com/docs.html
Start here.

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-- https://sites.google.com/site/earnieboyd

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Re: real beginer

wilson
In reply to this post by Trixie
Welcome to Cygwin Trixie.

If you visit the "Problems" link on the Cygwin home page
(http://cygwin.com/problems.html) you will see that there are some things
you can do to help the community diagnose your issue.  Please run the
cygcheck command and attach the output file (see the web page instructions)
as a plain text file to your response.  This will let the community see what
is installed and if you are missing anything.

Sincerely,

Brian S. Wilson
============================================================================
> I'm real beginner with cygwin, actually linux and everything related.
> But i need to instal and use certain fortran based program. I installed
> cygwin and several packages. I'm trying to call certain module and
> all i get is bash: module: command not found I googled it up and i
> found the solution that i should call /etc/profile.d/modules.sh
> before my module. but there is now module.sh in my /profile.d
> folder! Did i miss some package to install? What should i do? Please
> help! I desperately need to start that program :(((


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Re: real beginer

Eliot Moss
In reply to this post by Trixie
On 10/23/2012 9:28 AM, Trixie wrote:
> I'm real beginner with cygwin, actually linux and everything related.
> But i need to instal and use certain fortran based program. I installed
> cygwin and several packages. I'm trying to call certain module and all i get
> is
> bash: module: command not found
> I googled it up and i found the solution that i should call
> /etc/profile.d/modules.sh before my module. but there is now module.sh in my
> /profile.d folder! Did i miss some package to install? What should i do?
> Please help! I desperately need to start that program :(((

Dear Trixie:

cygwin does not magically bring all of Linux to the Windows environment.
Rather, it provides a library of Linux (posix, actually) calls that
allows many Linux programs to be re-built to run under Windows, including
bash (and other shells).  I do not see the module program as being
available as a regular cygwin package.  There is also a collection
of packages called cygport (more things ported to run under cygwin),
and I don't see it there either.  So it would appear that it has not
been ported.

However, it is generally something used with another program, the one
you really want to use, to help in setting up environment variables
such as your path.  So ... what is the program you really want to run?
We can see whether THAT program is available at all under cygwin.

It may or may not be difficult to port the module package to cygwin;
someone would have to try.  Many programs port, but not every aspect
of Linux appears in cygwin, so not everything ports, and the level of
effort needed varies.

Regards -- Eliot Moss


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Re: real beginer

Trixie
In reply to this post by Trixie
Thanks! This is really fast reply :) I feel already welcome here.
Ok i ran cygcheck and this is result. I hope i understood how to send you a file.
Program i need to use is  BigDFT 

cygwinhelpneeded.txt
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Re: real beginer

Christopher Faylor-8
On Tue, Oct 23, 2012 at 06:53:46AM -0700, Trixie wrote:
>Thanks! This is really fast reply :) I feel already welcome here.
>Ok i ran cygcheck and this is result. I hope i understood how to send you a
>file.
>Program i need to use is   BigDFT <http://inac.cea.fr/L_Sim/BigDFT/>  

It seems like you're putting the cart before the horse here.

If you're having problems running BigDFT you should be checking with them
first.  If they need Cygwin to run, then they should have some sort of
setup instructions.

>cygwinhelpneeded.txt
><http://cygwin.1069669.n5.nabble.com/file/n93902/cygwinhelpneeded.txt>  

That is not the output requested at http://cygwin.com/problems.html .  You
need to follow the instructions there exactly.  But, first, check with the
site which provides the software that you're trying to run.

cgf

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Re: real beginer

Andrew DeFaria-2
In reply to this post by Trixie
On 10/23/2012 06:28 AM, Trixie wrote:
> I'm real beginner with cygwin, actually linux and everything related.
> But i need to instal and use certain fortran based program. I installed
> cygwin and several packages. I'm trying to call certain module and all i get
> is
> bash: module: command not found
What is "module"? What's it supposed to be? Where did you get it? Where
did you install it to?

Execution of scripts/binaries in Cygwin is not very much unlike
execution of such commands in Windows cmd. The command name is searched
for using the PATH environment variable. The difference really is
Windows paths vs POSIX paths. That said, what do you see when you do
"echo $PATH" in your bash shell?
> I googled it up and i found the solution that i should call
> /etc/profile.d/modules.sh before my module. but there is now module.sh in my
> /profile.d folder! Did i miss some package to install? What should i do?
> Please help! I desperately need to start that program :(((
Later on you mention that "that program" is "BigDFT
<http://inac.cea.fr/L_Sim/BigDFT/>". This appears to be a package
distributed in source form. So now you have get it and build it. The
build instructions mention nothing about Cygwin at all. So, effectively,
you're talking about porting this program to Windows in the Cygwin
environment. This is a very ambitious project for somebody who
admittedly is a real beginner with Cygwin and Linux and everything
related. Not impossible but a very, very big thing.  The install
instructions talk about Fortran (so you'll need to install Fortran on
Cygwin if you plan to go further) and using Intel's Fortran compiler as
well as a C compiler. This is not a task for beginners unless they are
tenacious in their goal of getting this done.

I would highly recommend you contact the developers of BigDFT and ask if
they have considered porting it to Cygwin.
--
Andrew DeFaria <http://defaria.com>
And whose cruel idea was it to put an S in the word Lisp?


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Re: real beginer

Trixie
In reply to this post by Trixie
Thank you all.
Here's my story. I'm physics student and my master degree work is "Application of GPU on DFT calculations". I need this BigDFT to run certain examples on cuda based GPU computer and on regular CPU and discuss the results.
Cygwin was my first choice because i felt comfortable using it. But I think this is gonna be harder then i expected. I guees i should give up Cygwin and instal (maybe) UBUNTU on partition of my computer and try there. Any suggestion there?
Thank you all again, you've been most kind.
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Re: real beginer

Christopher Faylor-8
On Tue, Oct 23, 2012 at 07:31:41AM -0700, Trixie wrote:
>Thank you all.
>Here's my story. I'm physics student and my master degree work is
>"Application of GPU on DFT calculations". I need this BigDFT to run certain
>examples on cuda based GPU computer and on regular CPU and discuss the
>results.
>Cygwin was my first choice because i felt comfortable using it. But I think
>this is gonna be harder then i expected. I guees i should give up Cygwin and
>instal (maybe) UBUNTU on partition of my computer and try there. Any
>suggestion there?

If this is a linux-based package then you should, again, check with the
original web site for recommendations.  Any modern Linux is likely to be
ok but we can't advise you about Linux here.  That isn't something that
we do in this mailing list.

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Re: real beginer

Bill Meier
In reply to this post by Andrew DeFaria-2
On 10/23/2012 10:19 AM, Andrew DeFaria wrote:
> On 10/23/2012 06:28 AM, Trixie wrote:
>> I'm real beginner with cygwin, actually linux and everything related.
>> But i need to instal and use certain fortran based program. I installed
>> cygwin and several packages. I'm trying to call certain module and all

> Later on you mention that "that program" is "BigDFT
> <http://inac.cea.fr/L_Sim/BigDFT/>". This appears to be a package
> distributed in source form. So now you have get it and build it. The
> build instructions mention nothing about Cygwin at all.
>
> I would highly recommend you contact the developers of BigDFT and ask if
> they have considered porting it to Cygwin.

I agree with the previous poster.

Phrases like "massively parallel electronic structure code" and etc
suggest this is a large complex package probably making intensive use of
*nix functionality.

I suspect strongly doing a port would be a *big* project.

My 2c:

You'd probably be *far* better off getting access to a Linux system.

If you absolutely must use Windows, running the program on a Linux
virtual machine under Windows might work, but I would suspect that the
program may very well require "serious" hardware and might not run
effectively on a virtual machine.

As noted previously, the build process looks a bit complex so I'd also
suggest finding someone with Linux lnowledge to build and install the
system.


Bill Meier

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Re: real beginer

Eliot Moss
In reply to this post by Trixie
On 10/23/2012 10:31 AM, Trixie wrote:

> Thank you all.
> Here's my story. I'm physics student and my master degree work is
> "Application of GPU on DFT calculations". I need this BigDFT to run certain
> examples on cuda based GPU computer and on regular CPU and discuss the
> results.
> Cygwin was my first choice because i felt comfortable using it. But I think
> this is gonna be harder then i expected. I guees i should give up Cygwin and
> instal (maybe) UBUNTU on partition of my computer and try there. Any
> suggestion there?
> Thank you all again, you've been most kind.

I am most of the way through building bigdft under cygwin.  I have
no idea how the GPU aspect might work but here is what I've done
so far:

1) Download blas.tgz to ~/downloads (where I put things)
    In ~/tools (because I like it):
    tar xzvf ~/downloads/blas.tgz
    In ~/tools/BLAS:
    Edit make.inc as desired
    make
    cp blas_LINUX.a /usr/lib/libblas.a

2) Download lapack-3.4.2.tgz to ~/downloads
    In ~/tools, tar xzvf ~/downloads/lapack-3.4.2.tgz
    In ~/tools/lapack-3.4.2:
    cp make.inc.example make.inc
    Edit make.inc as desired; note that libblas.a is in /usr/lib, so
      you *must* edit that line
    make  [takes a LONG time]
    cp *.a /usr/lib

3) Download bigdft-1.6.0.tar.gz to ~/downloads
    In ~/tools, gunzip -c ~/downloads/bigdft-1.6.0.tar.gz | tar xvf -
    In ~/tools/bigdft-1.6.0:
    ./configure  (takes a while)
    make         (takes quite a while)

This ultimately failed when linking, so something seems missing or
slightly off. I will try to look at it later.

On the other hand, setting up a Linux partition, or using
a Linux virtual machine under Windows, are reasonable options too.

Eliot Moss


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Re: real beginer

marco atzeri-4
On 10/23/2012 6:35 PM, Eliot Moss wrote:

> On 10/23/2012 10:31 AM, Trixie wrote:
>> Thank you all.
>> Here's my story. I'm physics student and my master degree work is
>> "Application of GPU on DFT calculations". I need this BigDFT to run
>> certain
>> examples on cuda based GPU computer and on regular CPU and discuss the
>> results.
>> Cygwin was my first choice because i felt comfortable using it. But I
>> think
>> this is gonna be harder then i expected. I guees i should give up
>> Cygwin and
>> instal (maybe) UBUNTU on partition of my computer and try there. Any
>> suggestion there?
>> Thank you all again, you've been most kind.
>
> I am most of the way through building bigdft under cygwin.  I have
> no idea how the GPU aspect might work but here is what I've done
> so far:
>
> 1) Download blas.tgz to ~/downloads (where I put things)
>     In ~/tools (because I like it):
>     tar xzvf ~/downloads/blas.tgz
>     In ~/tools/BLAS:
>     Edit make.inc as desired
>     make
>     cp blas_LINUX.a /usr/lib/libblas.a
>
> 2) Download lapack-3.4.2.tgz to ~/downloads
>     In ~/tools, tar xzvf ~/downloads/lapack-3.4.2.tgz
>     In ~/tools/lapack-3.4.2:
>     cp make.inc.example make.inc
>     Edit make.inc as desired; note that libblas.a is in /usr/lib, so
>       you *must* edit that line
>     make  [takes a LONG time]
>     cp *.a /usr/lib

1 & 2 are already available on liblapack-devel

$ cygcheck -l liblapack-devel |grep "\.a"
/usr/lib/libblas.a
/usr/lib/libblas.dll.a
/usr/lib/liblapack.a
/usr/lib/liblapack.dll.a
/usr/lib/libtmglib.a


>
> 3) Download bigdft-1.6.0.tar.gz to ~/downloads
>     In ~/tools, gunzip -c ~/downloads/bigdft-1.6.0.tar.gz | tar xvf -
>     In ~/tools/bigdft-1.6.0:
>     ./configure  (takes a while)
>     make         (takes quite a while)
>
> This ultimately failed when linking, so something seems missing or
> slightly off. I will try to look at it later.
>
> On the other hand, setting up a Linux partition, or using
> a Linux virtual machine under Windows, are reasonable options too.
>
> Eliot Moss
>



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Re: real beginer

Sven Köhler-2
In reply to this post by Trixie
Am 23.10.2012 15:28, schrieb Trixie:
> I'm real beginner with cygwin, actually linux and everything related.
> But i need to instal and use certain fortran based program. I installed
> cygwin and several packages. I'm trying to call certain module and all i get
> is
> bash: module: command not found

I googled a bit about fortran, and it seems that "module" is a fortran
command. Note, that what you see when you open a cygwin window, is a
command shell (bash in this case), which allows you to execute certain
programs. It does not understand fortran commands.

I believe, you will have to install gcc's fortran compiler. Then you may
be able to compile and run fortran program. However, I'm not familiar
with that.

> I googled it up and i found the solution that i should call
> /etc/profile.d/modules.sh before my module. but there is now module.sh in my
> /profile.d folder! Did i miss some package to install? What should i do?
> Please help! I desperately need to start that program :(((

I'm sorry, but /etc/profile.d/modules.sh is totally unrelated to your
problem.

I strongly suggest, that you search for somebody that has experience
with Linux and fortran. Ask you supervisor if necessary. I assume, this
is work for you master thesis?

Eliot is trying to guide you through the process of building BigDFT. If
that works for you, that's fine. Then again, you should make sure that
BigDFT accesses the GPU it the most direct way possible, i.e. that it
doesn't have to pass the information through several layer of emulation.
With cygwin, there's a fair chance of that being the case.
I presume, you will do sort of benchmarking?


Regards,
  Sven


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Re: real beginer

Andrew DeFaria-2
In reply to this post by Eliot Moss
On 10/23/2012 9:35 AM, Eliot Moss wrote:

> On 10/23/2012 10:31 AM, Trixie wrote:
>> Thank you all.
>> Here's my story. I'm physics student and my master degree work is
>> "Application of GPU on DFT calculations". I need this BigDFT to run
>> certain
>> examples on cuda based GPU computer and on regular CPU and discuss the
>> results.
>> Cygwin was my first choice because i felt comfortable using it. But I
>> think
>> this is gonna be harder then i expected. I guees i should give up
>> Cygwin and
>> instal (maybe) UBUNTU on partition of my computer and try there. Any
>> suggestion there?
>> Thank you all again, you've been most kind.
>
> I am most of the way through building bigdft under cygwin.  I have
> no idea how the GPU aspect might work but here is what I've done
> so far:
>
> 1) Download blas.tgz to ~/downloads (where I put things)
>    In ~/tools (because I like it):
>    tar xzvf ~/downloads/blas.tgz
>    In ~/tools/BLAS:
>    Edit make.inc as desired
>    make
>    cp blas_LINUX.a /usr/lib/libblas.a
>
> 2) Download lapack-3.4.2.tgz to ~/downloads
>    In ~/tools, tar xzvf ~/downloads/lapack-3.4.2.tgz
>    In ~/tools/lapack-3.4.2:
>    cp make.inc.example make.inc
>    Edit make.inc as desired; note that libblas.a is in /usr/lib, so
>      you *must* edit that line
>    make  [takes a LONG time]
>    cp *.a /usr/lib
To run on Windows, shouldn't this .a files really be .dll's?

>
> 3) Download bigdft-1.6.0.tar.gz to ~/downloads
>    In ~/tools, gunzip -c ~/downloads/bigdft-1.6.0.tar.gz | tar xvf -
>    In ~/tools/bigdft-1.6.0:
>    ./configure  (takes a while)
>    make         (takes quite a while)
>
> This ultimately failed when linking, so something seems missing or
> slightly off. I will try to look at it later.
>
> On the other hand, setting up a Linux partition, or using
> a Linux virtual machine under Windows, are reasonable options too.
If you're using Cygwin's gcc/fortran and linker I suspect you'll need
.dll's not .a's.
--
Andrew DeFaria <http://defaria.com>
Madness takes its toll. Please have exact change.


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Re: real beginer

Trixie
This post was updated on .
In reply to this post by marco atzeri-4
I have liblapack-devel instaled and did ./configure and make . It took some time but it finished. Problem happened when i tried to do this tutorial . It says -bash: bigdft: command not found
 I read somethere i shoud first do module load bigdft, but when I do that, there is that module: command not found.
Currently I'm not using gpu (there is option to load cuda configure --enable-cuda-gpu) I'm just trying to make sure this thing works at all.
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Re: real beginer

Andrew DeFaria-2
On 10/23/2012 12:46 PM, Trixie wrote:
> I have liblapack-devel instaled and did ./configure and make . It took some
> time but it finished.
Did make finish successfully, returning a 0 status? Did you have a
bigdft.exe file? If you type "ls bigdft" do you see an executable?
(Note: The file's name is actually bigdft.exe but ls will list it as
bigdft).
>   Problem happened when i tried to do this  tutotial
> <http://inac.cea.fr/L_Sim/BigDFT/tutorials/H1A_first_run.html>   . It says
> -bash: bigdft: command not found
The tutorial shows you doing an ls and it listing out two files: bigdft
and posinp.xyz. Did you see those files? Cause your supposed to do that
*before* you type in "./bigdft | tee N2.out". And you did include "./"
before "bigdft" right?
> I read somethere i shoud first do module load bigdft, but when I do that,
> there is that module: command not found.
Module is not a command - period. The tutorial you pointed us to does
not say you need to first do "module load bigdft" - in fact the word
"module" does not appear on that page - so what lead you to believe you
should first use a non-existent module command?
> Currently I'm not using gpu (there is option to load cuda configure
> --enable-cuda-gpu) I'm just trying to make sure this thing works at all.
--
Andrew DeFaria <http://defaria.com>
I got a new shadow. I had to get rid of the other one -- it wasn't doing
what I was doing.


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Re: real beginer

Trixie
This post was updated on .
<quote author="Andrew DeFaria-2">
On 10/23/2012 12:46 PM, Trixie wrote:
>> I have liblapack-devel instaled and did ./configure and make . It took some
>> time but it finished.
>Did make finish successfully, returning a 0 status? Did you have a
>bigdft.exe file? If you type "ls bigdft" do you see an executable?
>(Note: The file's name is actually bigdft.exe but ls will list it as
>bigdft).

i type ls bigdft and there's "No such file or directory" and i cant find bigdft.exe file anywhere. That means install and make didnt finish well, right?
posinp.xyz is there.


>   Problem happened when i tried to do this  tutotial
> <http://inac.cea.fr/L_Sim/BigDFT/tutorials/H1A_first_run.html>   . It says
> -bash: bigdft: command not found
The tutorial shows you doing an ls and it listing out two files: bigdft
and posinp.xyz. Did you see those files? Cause your supposed to do that
*before* you type in "./bigdft | tee N2.out". And you did include "./"
before "bigdft" right?
> I read somethere i shoud first do module load bigdft, but when I do that,
> there is that module: command not found.
Module is not a command - period. The tutorial you pointed us to does
not say you need to first do "module load bigdft" - in fact the word
>"module" does not appear on that page - so what lead you to believe you
>should first use a non-existent module command?

I googled it somewhere, some instruction at some laboratory that used BigDFT. I was getting really desperate. you can't blame girl for trying :)

> Currently I'm not using gpu (there is option to load cuda configure
> --enable-cuda-gpu) I'm just trying to make sure this thing works at all.
--
Andrew DeFaria <http://defaria.com>
I got a new shadow. I had to get rid of the other one -- it wasn't doing
what I was doing.

Sooo...as far as i understand now, something wrong was with install and make and i didn't get bigdft.exe file. there is bigdft.pc in folder i compiled but no .exe . You are returning me hope i can finish this in time!


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Re: real beginer

Andrew DeFaria-2
On 10/23/2012 2:46 PM, Trixie wrote:

> On 10/23/2012 12:46 PM, Trixie wrote:
>>> I have liblapack-devel instaled and did ./configure and make . It took
>>> some
>>> time but it finished.
>> Did make finish successfully, returning a 0 status? Did you have a
>> bigdft.exe file? If you type "ls bigdft" do you see an executable?
>> (Note: The file's name is actually bigdft.exe but ls will list it as
>> bigdft).
> /i type ls bigdft and there's "No such file or directory" and i cant find
> bigdft.exe file anywhere. That means install and make didnt finish well,
> right?
Probably. You could do something like: make; echo "Status from make was $?"

The $? is the return status from the previous command. That will only
tell you if the make turned 0 for success. The output of make would be
much more instructive.
> posinp.xyz is there./
AFAICT posinp.xyz is not produced from the make.

You really should approach the people who maintain this package and ask
them about it. This package is not Cygwin.
--
Andrew DeFaria <http://defaria.com>
By the time you make ends meet, they move the ends.


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Re: real beginer

Trixie

>>> I have liblapack-devel instaled and did ./configure and make . It took
>>> some
>>> time but it finished.
>> Did make finish successfully, returning a 0 status? Did you have a
> >> bigdft.exe file? If you type "ls bigdft" do you see an executable?
> >> (Note: The file's name is actually bigdft.exe but ls will list it as
> >> bigdft).
> > /i type ls bigdft and there's "No such file or directory" and i cant find
> > bigdft.exe file anywhere. That means install and make didnt finish well,
> > right?
> Probably. You could do something like: make; echo "Status from make was $?"

> The $? is the return status from the previous command. That will only
> tell you if the make turned 0 for success. The output of make would be
> much more instructive.

Nope, it didnt turned 0. it is 2. Status from make was 2.


> You really should approach the people who maintain this package and ask
> them about it. This package is not Cygwin.

Yes i see that now. Unfortunately i lost two weeks with this. Well, my next step is to contact someone in charge of BigDFT and ask for help.
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Re: real beginer

Eliot Moss
On 10/23/2012 6:35 PM, Trixie wrote:

>
>>>> I have liblapack-devel instaled and did ./configure and make . It took
>>>> some
>>>> time but it finished.
>>> Did make finish successfully, returning a 0 status? Did you have a
>>>> bigdft.exe file? If you type "ls bigdft" do you see an executable?
>>>> (Note: The file's name is actually bigdft.exe but ls will list it as
>>>> bigdft).
>>> /i type ls bigdft and there's "No such file or directory" and i cant
>> find
>>> bigdft.exe file anywhere. That means install and make didnt finish well,
>>> right?
>> Probably. You could do something like: make; echo "Status from make was
>> $?"

Ok, so here is one thing I have found out.

This package has init/locreg.f90 in one directory
and linear/locReg.f90 in another.  It places the .o
in the *same* directory.  The underlying Windows
file system does not support locreg.o and locReg.o
(names that differ in upper vs. lower case only)
in the same directory.  I am trying renaming one
of the files and manually changing the makefile
to see if it will build with suitable resolved
names.  But this is probably what happened to you,
and should be referred upstream to the purveyors
of the package.  It's an 'evil' thing to do because
it is not portable to platforms such as this and
tends to be confusing even on platforms where it
works ...

More once I see if where this change gets me ...

Eliot Moss

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