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]]
The Cygwin is the problem. I am redoing and will let you know how it goes. Thanks for your help. Sincerely, Erin 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 >-- Erin Hodgess, PhD mailto: erinm.hodgess at gmail.com [[alternative HTML version deleted]]
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? 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]]
>>>>> 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