64bit linux kernel + 32bit userland: computation error


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Message 31953 - Posted: 11 Aug 2013, 15:42:14 UTC

After long absence and a move from gent0o 64bit to debian 32bit userland + 64bit kernel and to a nice GeForce GTX 460 I just wanted to pick up GPU crunching again, but something is very wrong. Every task fails right after downloading the project files.. WCG and malariacontrol work fine, both happily running 64bit apps.


==> stdoutdae.txt <== 
11-Aug-2013 17:01:20 [GPUGRID] Finished download of libcufft.so.4.2.9 
11-Aug-2013 17:01:21 [GPUGRID] Starting task 16x1-SANTI_RAP74wt-8-34-RND6971_1 using acemdlong version 618 (cuda42) in slot 4 

==> stderrdae.txt <== 
mv: cannot stat 'slots/4/COLVAR': No such file or directory 
mv: cannot stat 'slots/4/COLVAR': No such file or directory 
mv: cannot stat 'slots/4/COLVAR': No such file or directory 
mv: cannot stat 'slots/4/COLVAR': No such file or directory 
mv: cannot stat 'slots/4/COLVAR': No such file or directory 
mv: cannot stat 'slots/4/COLVAR': No such file or directory 
mv: cannot stat 'slots/4/COLVAR': No such file or directory 
mv: cannot stat 'slots/4/COLVAR': No such file or directory 
mv: cannot stat 'slots/4/log.file': No such file or directory 
mv: cannot stat 'slots/4/log.file': No such file or directory 
mv: cannot stat 'slots/4/log.file': No such file or directory 
mv: cannot stat 'slots/4/log.file': No such file or directory 
mv: cannot stat 'slots/4/log.file': No such file or directory 
mv: cannot stat 'slots/4/log.file': No such file or directory 
mv: cannot stat 'slots/4/log.file': No such file or directory 

==> stdoutdae.txt <== 
11-Aug-2013 17:01:22 [GPUGRID] Computation for task 16x1-SANTI_RAP74wt-8-34-RND6971_1 finished 
11-Aug-2013 17:01:22 [GPUGRID] Output file 16x1-SANTI_RAP74wt-8-34-RND6971_1_0 for task 16x1-SANTI_RAP74wt-8-34-RND6971_1 absent 
11-Aug-2013 17:01:22 [GPUGRID] Output file 16x1-SANTI_RAP74wt-8-34-RND6971_1_1 for task 16x1-SANTI_RAP74wt-8-34-RND6971_1 absent 
11-Aug-2013 17:01:22 [GPUGRID] Output file 16x1-SANTI_RAP74wt-8-34-RND6971_1_2 for task 16x1-SANTI_RAP74wt-8-34-RND6971_1 absent 
11-Aug-2013 17:01:22 [GPUGRID] Output file 16x1-SANTI_RAP74wt-8-34-RND6971_1_3 for task 16x1-SANTI_RAP74wt-8-34-RND6971_1 absent 
11-Aug-2013 17:01:35 [GPUGRID] Started upload of 16x1-SANTI_RAP74wt-8-34-RND6971_1_7 
11-Aug-2013 17:01:36 [GPUGRID] Finished upload of 16x1-SANTI_RAP74wt-8-34-RND6971_1_7 
11-Aug-2013 17:02:55 [GPUGRID] Sending scheduler request: To report completed tasks. 
11-Aug-2013 17:02:55 [GPUGRID] Reporting 1 completed tasks 
11-Aug-2013 17:02:55 [GPUGRID] Requesting new tasks for NVIDIA 



# ldd -v -d -r /var/lib/boinc-client/projects/www.gpugrid.net/*.so.*
libcudart.so.4.2.9:
        linux-vdso.so.1 (0x00007fff259fe000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f9e32958000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f9e3273c000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f9e32534000)
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f9e3222c000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9e31f2d000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f9e31d17000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9e3196b000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f9e32e0a000)

        Version information:
        ./libcudart.so.4.2.9:
                libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
                libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
                libstdc++.so.6 (CXXABI_1.3.1) => /usr/lib64/libstdc++.so.6
                libstdc++.so.6 (CXXABI_1.3) => /usr/lib64/libstdc++.so.6
                libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib64/libstdc++.so.6
                libc.so.6 (GLIBC_2.7) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
                libpthread.so.0 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libpthread.so.0
                libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
        /lib/x86_64-linux-gnu/libdl.so.2:
                ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
                libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /lib/x86_64-linux-gnu/libpthread.so.0:
                ld-linux-x86-64.so.2 (GLIBC_2.2.5) => /lib64/ld-linux-x86-64.so.2
                ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
                ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
                libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /lib/x86_64-linux-gnu/librt.so.1:
                libpthread.so.0 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libpthread.so.0
                libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
                libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /usr/lib64/libstdc++.so.6:
                ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
                libm.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libm.so.6
                libgcc_s.so.1 (GCC_4.2.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
                libgcc_s.so.1 (GCC_3.3) => /lib/x86_64-linux-gnu/libgcc_s.so.1
                libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
                libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.17) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /lib/x86_64-linux-gnu/libm.so.6:
                libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /lib/x86_64-linux-gnu/libgcc_s.so.1:
                libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /lib/x86_64-linux-gnu/libc.so.6:
                ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
                ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
libcufft.so.4.2.9:
        linux-vdso.so.1 (0x00007fff0d7a1000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f24d4011000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f24d3df5000)
        libcudart.so.4 => not found
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f24d3aed000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f24d37ee000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f24d35d8000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f24d322c000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f24d6291000)
undefined symbol: cudaPeekAtLastError   (./libcufft.so.4.2.9)
undefined symbol: cudaFree      (./libcufft.so.4.2.9)
undefined symbol: __cudaRegisterVar     (./libcufft.so.4.2.9)
undefined symbol: cudaEventDestroy      (./libcufft.so.4.2.9)
undefined symbol: __cudaRegisterFunction        (./libcufft.so.4.2.9)
undefined symbol: cudaGetLastError      (./libcufft.so.4.2.9)
undefined symbol: cudaMemcpyToSymbolAsync       (./libcufft.so.4.2.9)
undefined symbol: cudaStreamWaitEvent   (./libcufft.so.4.2.9)
undefined symbol: cudaGetDevice (./libcufft.so.4.2.9)
undefined symbol: cudaGetExportTable    (./libcufft.so.4.2.9)
undefined symbol: cudaEventSynchronize  (./libcufft.so.4.2.9)
undefined symbol: cudaSetupArgument     (./libcufft.so.4.2.9)
undefined symbol: cudaConfigureCall     (./libcufft.so.4.2.9)
undefined symbol: __cudaUnregisterFatBinary     (./libcufft.so.4.2.9)
undefined symbol: cudaLaunch    (./libcufft.so.4.2.9)
undefined symbol: cudaFuncSetCacheConfig        (./libcufft.so.4.2.9)
undefined symbol: cudaGetDeviceProperties       (./libcufft.so.4.2.9)
undefined symbol: cudaEventCreate       (./libcufft.so.4.2.9)
undefined symbol: cudaUnbindTexture     (./libcufft.so.4.2.9)
undefined symbol: __cudaRegisterFatBinary       (./libcufft.so.4.2.9)
undefined symbol: __cudaRegisterTexture (./libcufft.so.4.2.9)
undefined symbol: cudaCreateChannelDesc (./libcufft.so.4.2.9)
undefined symbol: cudaBindTexture       (./libcufft.so.4.2.9)
undefined symbol: cudaMemcpy    (./libcufft.so.4.2.9)
undefined symbol: cudaFuncGetAttributes (./libcufft.so.4.2.9)
undefined symbol: cudaMalloc    (./libcufft.so.4.2.9)
undefined symbol: cudaEventRecord       (./libcufft.so.4.2.9)

        Version information:
        ./libcufft.so.4.2.9:
                libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
                libm.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libm.so.6
                libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
                libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib64/libstdc++.so.6
                libstdc++.so.6 (CXXABI_1.3) => /usr/lib64/libstdc++.so.6
                libc.so.6 (GLIBC_2.7) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
                libpthread.so.0 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libpthread.so.0
                libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
        /lib/x86_64-linux-gnu/libdl.so.2:
                ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
                libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /lib/x86_64-linux-gnu/libpthread.so.0:
                ld-linux-x86-64.so.2 (GLIBC_2.2.5) => /lib64/ld-linux-x86-64.so.2
                ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
                ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
                libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /usr/lib64/libstdc++.so.6:
                ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
                libm.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libm.so.6
                libgcc_s.so.1 (GCC_4.2.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
                libgcc_s.so.1 (GCC_3.3) => /lib/x86_64-linux-gnu/libgcc_s.so.1
                libgcc_s.so.1 (GCC_3.0) => /lib/x86_64-linux-gnu/libgcc_s.so.1
                libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.3) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.17) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /lib/x86_64-linux-gnu/libm.so.6:
                libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /lib/x86_64-linux-gnu/libgcc_s.so.1:
                libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
                libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
        /lib/x86_64-linux-gnu/libc.so.6:
                ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
                ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2

What could be the problem? Installing libcuda1:amd64 didn't improve anything.
#Regards.
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Message 31964 - Posted: 12 Aug 2013, 16:54:14 UTC - in response to Message 31953.  

After long absence and a move from gent0o 64bit to debian 32bit userland + 64bit kernel and to a nice GeForce GTX 460 I just wanted to pick up GPU crunching again, but something is very wrong. Every task fails right after downloading the project files.. WCG and malariacontrol work fine, both happily running 64bit apps.


GPUGrid requires an x64 version of Linux. My guess is that debian 32bit is the problem. Why go with "32bit userland + 64bit kernel"? Bad Gentoo experiences?
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Message 32019 - Posted: 15 Aug 2013, 22:15:42 UTC - in response to Message 31964.  

Well free software is about freedom of choice, isn't it? I had to pick a 64bit-kernel to satisfy the android build chain. But as cross-grading a debian system is not supported and I was not in the mood to break my libc and everything that depends on it (like: *EVERYTHING*, apart from busybox-static), and also don't want the heavier memory usage which comes just from 64bit pointers, I didn't fully migrate to 64bit userland. However I have libc6:amd64 installed and the other BOINC apps do just fine with 64bit executables.
I think it is just that the LD_LIBRARY_PATH is not being set to the gpugrid working directory and/or the missing symlink 
‘libcudart.so.4’ -> ‘libcudart.so.4.2.9’
because with these ldd doesn't complain any more.
But because there is no error output apart from 
mv: cannot stat 'slots/4/COLVAR': No such file or directory
it is hard to even understand what is going wrong...
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Message 32100 - Posted: 20 Aug 2013, 17:24:36 UTC - in response to Message 31953.  

Hello,

Regrettably, with your unique OS configuration there is no practical way that we can help you solve your problem, beyond observing that the incomplete 64-bit user-space is almost certainly a contributing factor.

MJH
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Message 33653 - Posted: 28 Oct 2013, 12:51:58 UTC

Be as it may, even when running a 32bit kernel, I can not make it crunch a work unit. Keeps telling me
28-Oct-2013 13:51:28 [GPUGRID] update requested by user
28-Oct-2013 13:51:32 [GPUGRID] Sending scheduler request: Requested by user.
28-Oct-2013 13:51:32 [GPUGRID] Requesting new tasks for NVIDIA
28-Oct-2013 13:51:34 [GPUGRID] Scheduler request completed: got 0 new tasks
28-Oct-2013 13:51:34 [GPUGRID] No tasks sent

Is my account downtrusted because it failed to finish any WUs?
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Message 33665 - Posted: 29 Oct 2013, 17:14:34 UTC - in response to Message 33653.  

You need a 64bit Linux everything. The apps are designed for 64bit only. There are no 32bit apps for Linux.
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