From m@ech|er @end|ng |rom @t@t@m@th@ethz@ch  Mon Mar  4 10:06:11 2019
From: m@ech|er @end|ng |rom @t@t@m@th@ethz@ch (Martin Maechler)
Date: Mon, 4 Mar 2019 10:06:11 +0100
Subject: [Rd] Problem with compiling OpenBLAS to work with R
In-Reply-To: <CACxE24=hVLA8gUucL=d09SV7eY-E7s6RH6AeTKFjdddNYU70pw@mail.gmail.com>
References: <CACxE24kZSEVgfah=fGXqx0jzrGoc6RBwUSgBWTMgoyi4q0z84A@mail.gmail.com>
 <CAPekMCkox-bmcVjZbn2uNE5AipWkbdVg7-C=QddEhDhNUU830w@mail.gmail.com>
 <CAL6gwn+hEg8BJBFOuksEQyvQXknzdFpTpHmTZ080wrAeoWA-Hw@mail.gmail.com>
 <CACxE24=hVLA8gUucL=d09SV7eY-E7s6RH6AeTKFjdddNYU70pw@mail.gmail.com>
Message-ID: <23676.60035.254296.166127@stat.math.ethz.ch>

>>>>> 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
    >>> 
    >> --
    >> Sent from Gmail Mobile
    >> 

    > 	[[alternative HTML version deleted]]

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] Problem with compiling OpenBLAS to work with R
Martin Maechler