From er|nm@hodge@@ @end|ng |rom gm@||@com  Mon Mar  4 11:03:03 2019
From: er|nm@hodge@@ @end|ng |rom gm@||@com (Erin Hodgess)
Date: Mon, 4 Mar 2019 03:03:03 -0700
Subject: [Rd] Problem with compiling OpenBLAS to work with R
In-Reply-To: <23676.60035.254296.166127@stat.math.ethz.ch>
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Message-ID: <CACxE24ndEWQyMAaztNFR8mnOp-=p9a_3510r_j27em3i_qFOAg@mail.gmail.com>

I actually figured it out.  I went back in any changed the mean difference
from 2-e12 to 5e-12.

Thanks,
Erin

Erin Hodgess, PhD
mailto: erinm.hodgess at gmail.com


On Mon, Mar 4, 2019 at 2:10 AM Martin Maechler <maechler at stat.math.ethz.ch>
wrote:

> >>>>> Erin Hodgess
> >>>>>     on Fri, 1 Mar 2019 12:30:35 -0700 writes:
>
>     > Yay!  I re-installed everything and got through "Make
>     > distribution"!  I have one more question, please: I am
>     > running the make check-all.  I have an error at reg-1d.
>     > It stops the process.  However, the mean difference (as
>     > per the file) is 2.0e-12.  I'm ok with that.  How do I
>     > bypass this, please?
>
> If you'd be really precise in your report (use correct file
> names; show the exact error message + context lines of the *.Rout.fail
> file) I could help you.
>
> Note (by the way) that this may be yet another example showing
> that OpenBLAS may be faster but less accurate than the
> (plain+ minor tweaks) version of BLAS that ships with R.
>
> Martin
>
>     > Thanks, Erin
>
>     > Erin Hodgess, PhD mailto: erinm.hodgess at gmail.com
>
>
>     > On Wed, Feb 27, 2019 at 10:22 PM Avraham Adler
>     > <avraham.adler at gmail.com> wrote:
>
>     >> I believe that repo just follows the directions on my
>     >> blog. Without seeing Dr. Hodges?s code, my initial
>     >> concern is the many references to Cygwin. My method
>     >> specifically does not use Cygwin but MSYS2 and
>     >> Mingw64/Rtools35.  That will likely change to solely
>     >> Rtools40 once R3.6 is released due to the Msys system
>     >> being built in to it.
>     >>
>     >> There may be some library conflicts between Cygwin and
>     >> msys2/mingw64. If possible, my suggestion would be
>     >> uninstall everything and then just install msys2 (and add
>     >> in make after you to the first msys update) and rtools35.
>     >> Then there should be no conflicting libraries.
>     >>
>     >> Thanks,
>     >>
>     >> Avi
>     >>
>     >> On Thu, Feb 28, 2019 at 12:11 AM Kenny Bell
>     >> <kmbell56 at gmail.com> wrote:
>     >>
>     >>> This person has had apparent success - you could follow
>     >>> what they did or just download their product (with
>     >>> appropriate caution downloading a random .exe).
>     >>>
>     >>> https://github.com/thequackdaddy/R-OpenBLAS
>     >>>
>     >>> On Thu, Feb 28, 2019 at 6:28 AM Erin Hodgess
>     >>> <erinm.hodgess at gmail.com> wrote:
>     >>>
>     >>> > Hello!
>     >>> >
>     >>> > I'm not sure if this is the right place to post this,
>     >>> so apologies > in advance if I'm not in the right list.
>     >>> >
>     >>> > I downloaded the OpenBLAS and am following Avraham
>     >>> Adler's great > instructions.  However, when I run make,
>     >>> things go well to a certain point, > and then go bad:
>     >>> >
>     >>> > make > [snip]
>     >>> >
>     >>> > touch cygopenblas_haswellp-r0.3.5.a > make -j 1 -C
>     >>> test all > make[1]: Entering directory >
>     >>> '/home/erinm/OPB_HOME/xianyi-OpenBLAS-eebc189/test' >
>     >>> gfortran -O2 -Wall -frecursive -m64 -mavx2 -o sblat1
>     >>> sblat1.o > ../cygopenblas_haswellp-r0.3.5.a
>     >>> -L/usr/lib/gcc/x86_64-pc-msys/7.3.0
>     >>> >
>     >>>
> -L/usr/lib/gcc/x86_64-pc-msys/7.3.0/../../../../x86_64-pc-msys/lib/../lib
>     >>> > -L/usr/lib/../lib >
>     >>> -L/usr/lib/gcc/x86_64-pc-msys/7.3.0/../../../../x86_64-pc-msys/lib
>     >>> > -L/usr/lib/w32api -lmsys-2.0 >
>     >>>
> D:/msys64/usr/lib/../lib/libpthread.a(t-d001088.o):fake:(.text+0x2):
>     >>> > undefined reference to `__imp_pthread_mutex_destroy' >
>     >>>
> D:/msys64/usr/lib/../lib/libpthread.a(t-d001090.o):fake:(.text+0x2):
>     >>> > undefined reference to `__imp_pthread_mutex_init' >
>     >>>
> D:/msys64/usr/lib/../lib/libpthread.a(t-d001091.o):fake:(.text+0x2):
>     >>> > undefined reference to `__imp_pthread_mutex_lock' >
>     >>>
> D:/msys64/usr/lib/../lib/libpthread.a(t-d001094.o):fake:(.text+0x2):
>     >>> > undefined reference to `__imp_pthread_mutex_trylock' >
>     >>>
> D:/msys64/usr/lib/../lib/libpthread.a(t-d001095.o):fake:(.text+0x2):
>     >>> > undefined reference to `__imp_pthread_mutex_unlock' >
>     >>> collect2.exe: error: ld returned 1 exit status >
>     >>> make[1]: *** [Makefile:134: sblat1] Error 1 > make[1]:
>     >>> Leaving directory >
>     >>> '/home/erinm/OPB_HOME/xianyi-OpenBLAS-eebc189/test' >
>     >>> make: *** [Makefile:124: tests] Error 2
>     >>> >
>     >>> >
>     >>> > I think it has something to do with the
>     >>> threads/pthreads but am not sure > how to fix it.  Any
>     >>> suggestions much appreciated.
>     >>> >
>     >>> > Thanks, > Sincerely, > Erin
>     >>> >
>     >>> > Erin Hodgess, PhD > mailto: erinm.hodgess at gmail.com
>     >>> >
>     >>> > [[alternative HTML version deleted]]
>     >>> >
>     >>> > ______________________________________________ >
>     >>> R-devel at r-project.org mailing list >
>     >>> https://stat.ethz.ch/mailman/listinfo/r-devel
>     >>> >
>     >>>
>     >>> [[alternative HTML version deleted]]
>     >>>
>     >>> ______________________________________________
>     >>> R-devel at r-project.org mailing list
>     >>> https://stat.ethz.ch/mailman/listinfo/r-devel
>     >>>
>     >> --
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>     >>
>
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>
>     > ______________________________________________
>     > R-devel at r-project.org mailing list
>     > https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Rd] Problem with compiling OpenBLAS to work with R
Erin Hodgess