I think I still am getting seg faults on attempt to multiply matrices even
without conversion back (larger arguments, 3k x 1k)
I re-wrote another alternative transformation procedure and see nothing
wrong with it. Both Andrew's code and mine fail with the same symptoms.
Karl, can we verify assumptions about the format:
(1) the compressed_marix.set method expects host memory pointers.
(2) the format is compressed row storage (CSR). Documentation never says
explicitly that, and actually seems to have errors in size of elements and
jumper arrays (it says jumper array has to be cols+1 long wheres in CSR it
shoud actually be rows + 1 long, right? )
(3) the element sizes of jumper and column indices arrays are 32 bit and
are in little endian order (at least for the open MP backend).
Right now I can't even get open mp sparse multiplication work although CSR
format is not rocket science at all. Don't see a problem anywhere. Tried to
read Vienna's code to converm the assumptions above, but this seems to be
pretty elusive for the time being.
On Fri, Jul 22, 2016 at 10:26 AM, Andrew Palumbo <ap....@outlook.com> wrote:
> Yep thats it. Oh wow- well thats just embarrassing [image: 😊].
>
>
> Thanks very much for your time, Karl- much appreciated.
>
>
> Andy
> ------------------------------
> *From:* Karl Rupp <r...@iue.tuwien.ac.at>
> *Sent:* Friday, July 22, 2016 12:39:20 PM
> *To:* Andrew Palumbo; viennacl-devel
> *Subject:* Re: [ViennaCL-devel] Copying Values out of a compressed_matrix
>
> Hi,
>
> your second and third arguments to memory_read() are incorrect:
> The second argument is the offset from the beginning, the third argument
> is the number of bytes to be read. Shifting the zero to the second
> position fixes the snippet (plus correcting the loop bounds when
> printing at the end) :-)
>
> Best regards,
> Karli
>
>
>
> On 07/22/2016 08:51 AM, Andrew Palumbo wrote:
> > a couple of small mistakes in the previous c++ file:
> >
> >
> > The memory_read(..) call should be:
> >
> >
> > // read data back into our product buffers
> > viennacl::backend::memory_read(handle1, product_size_row * 4, 0,
> > product_row_ptr, false);
> > viennacl::backend::memory_read(handle2, product_NNz * 4, 0,
> > product_col_ptr, false);
> > viennacl::backend::memory_read(handle, product_NNz * 8, 0,
> > product_values_ptr, false);
> >
> >
> > (read product_NNz * x bytes instead of product_size_row * x)
> >
> >
> > I've attached the corrected file.
> >
> >
> > Thanks
> >
> >
> > Andy
> >
> > ------------------------------------------------------------------------
> > *From:* Andrew Palumbo <ap....@outlook.com>
> > *Sent:* Thursday, July 21, 2016 11:03:59 PM
> > *To:* Karl Rupp; viennacl-devel
> > *Subject:* Re: [ViennaCL-devel] Copying Values out of a compressed_matrix
> >
> > Hello,
> >
> >
> > I've mocked up a sample of the compressed_matrix multiplication that
> > I've been working with javacpp on in C++. I am seeing the same type of
> > memory errors when I try to read the data out of product, and into the
> > output buffers as I was with javacpp. By printing the matrix to stdout
> > as in the compressed_matrix example we can see that there are values
> > there, and they seem reasonable, but when i use
> > backend::memory_read(...) to retrive the buffers, I'm getting values
> > consistent with a memory error, and similar to what i was seeing in the
> > javacpp code. Maybe I am not using the handles correctly? Admittedly
> > my C++ is more than rusty, but I believe I am referencing the buffers
> > correctly in the output.
> >
> >
> > Below is the output of the attached file: sparse.cpp
> >
> >
> > Thanks very much,
> >
> >
> > Andy
> >
> >
> >
> > ViennaCL: compressed_matrix of size (10, 10) with 24 nonzeros:
> > (1, 2) 0.329908
> > (1, 3) 0.0110522
> > (1, 4) 0.336839
> > (2, 5) 0.0150778
> > (2, 7) 0.0143518
> > (3, 3) 0.217256
> > (3, 6) 0.346854
> > (3, 9) 0.45353
> > (4, 3) 0.407954
> > (4, 6) 0.651308
> > (5, 2) 0.676061
> > (5, 3) 0.0226486
> > (5, 4) 0.690264
> > (6, 5) 0.0998838
> > (6, 7) 0.0950744
> > (7, 2) 0.346173
> > (7, 3) 0.0115971
> > (7, 4) 0.353446
> > (7, 9) 0.684458
> > (8, 5) 0.0448123
> > (8, 7) 0.0426546
> > (8, 9) 0.82782
> > (9, 5) 0.295356
> > (9, 7) 0.281134
> >
> > row jumpers: [
> > -36207072,32642,-39708721,32642,6390336,0,2012467744,32767,2012467968
> ,32767,4203729,]
> > col ptrs: [
> >
> 0,0,-39655605,32642,-36207072,32642,6390336,0,10,0,-39672717,32642,2012466352,32767,-32892691,32642,1,0,6390336,0,2012466344,32767,60002304,2059362829,]
> > elements: [
> >
> 0.289516,0.304161,0.795779,0.334456,0.935264,0.585813,0.871237,0.811508,0.828558,0.0271863,6.92683e-310,6.92683e-310,1.061e-313,1.061e-313,6.36599e-314,4.24399e-314,6.36599e-314,6.92683e-310,4.24399e-314,1.2732e-313,2.122e-313,6.95324e-310,0.406537,0.0495716,0.370862,]
> >
> >
> > and similarly for multiplication of 2 1x1 matrices:
> >
> > Result:
> >
> > ViennaCL: compressed_matrix of size (1, 1) with 1 nonzeros:
> > (0, 0) 0.117699
> >
> > row jumpers: [
> > -717571424,32767,]
> > col ptrs: [
> > 6386240,]
> > elements: [
> > 0.289516,6.9479e-310,]
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> > *From:* Andrew Palumbo <ap....@outlook.com>
> > *Sent:* Wednesday, July 20, 2016 5:40:31 PM
> > *To:* Karl Rupp; viennacl-devel
> > *Subject:* Re: [ViennaCL-devel] Copying Values out of a compressed_matrix
> >
> > Oops, sorry about not cc'ing all.
> >
> >
> > I do not get correct data back for a (Random.nextDouble() populated) 1 x
> > 1 Matrix.
> >
> >
> > A:
> >
> > Row Pointer: [0, 1 ]
> >
> > Col Pointer: [0 ]
> > element Pointer: [0.6465821602909256 ]
> >
> >
> > B:
> >
> >
> > Row Pointer: [0, 1 ]
> > Col Pointer: [0 ]
> > element Pointer: [0.9513577109193919 ]
> >
> >
> > C = A %*% B
> >
> > Row Pointer: [469762248, 32632]
> > Col Pointer: [469762248 ]
> > element Pointer: [6.9245198744523E-310 ]
> >
> >
> > ouch.
> >
> >
> > It looks like I'm not copying the Buffers correctly at all. I'm may be
> > using the javacpp buffers incorrectly here, or I have possibly wrapped
> > the viennacl::backend::memory_handle class incorrectly, so I'm using a
> > pointer to the wrong memory from eg. viennacl::compressed_matrix::handle.
> >
> >
> > I mentioned before that the multiplication completed in on small <~300 x
> > 300 matrices because if I try to multiply two larger sparse matrices, an
> > err the JVM crashes with a SIGSEGV.
> >
> >
> > Since this code is all wrapped with javacpp, I don't really have a small
> > sample that I can show you (not going to dump a whole bunch of code on
> > you).
> >
> >
> > I'll keep trying to figure it out. Pretty sure the problem is on my end
> > here �� I really mainly wanted to ask you if I was using the correct
> > methods at this point, or if there was anything very obviously that I
> > was doing wrong.
> >
> >
> > Thanks a lot for your help!
> >
> >
> > Andy
> >
> >
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> > *From:* Karl Rupp <r...@iue.tuwien.ac.at>
> > *Sent:* Wednesday, July 20, 2016 5:00:36 PM
> > *To:* Andrew Palumbo; viennacl-devel
> > *Subject:* Re: [ViennaCL-devel] Copying Values out of a compressed_matrix
> > Hi,
> >
> > please keep viennacl-devel in CC:
> >
> > Just to clarify: Do you get incorrect values for a 1-by-1 matrix as
> > indicated in your sample data? In your previous email you mentioned that
> > results are fine for small matrices...
> >
> > I'm afraid I can only guess at the source of the error with the
> > informations provided. Any chance that you can provide a standalone code
> > to reproduce the problem with reasonable effort?
> >
> > Best regards,
> > Karli
> >
> >
> >
> > On 07/20/2016 10:16 PM, Andrew Palumbo wrote:
> >> Thanks so much for your quick answer!
> >>
> >>
> >> I actually am sorry to say that I made a mistake when writing the last
> >> email, I copied the wrong signature from the VCL documentation, and then
> >> the mistake propagated through the rest of the e-mail.
> >>
> >>
> >> I am actually using viennacl::backend::memory_read().
> >>
> >>
> >> Eg, for the row_jumpers and column_idx I read use:
> >>
> >> @Name("backend::memory_read")
> >> public static native void memoryReadInt(@Const @ByRef MemHandle
> src_buffer,
> >> int bytes_to_read,
> >> int offset,
> >> IntPointer ptr,
> >> boolean async);
> >>
> >> and for the Values:
> >>
> >>
> >> @Name("backend::memory_read")
> >> public static native void memoryReadDouble(@Const @ByRef MemHandle
> src_buffer,
> >> int bytes_to_read,
> >> int offset,
> >> DoublePointer ptr,
> >> boolean async);
> >>
> >> And then call:
> >>
> >>
> >> memoryReadInt(row_ptr_handle, (m +1) *4,0, row_ptr,false)
> >> memoryReadInt(col_idx_handle, NNz *4,0,col_idx,false)
> >> memoryReadDouble(element_handle, NNz *8,0, values,false)
> >>
> >>
> >> and after convetring them to java.nio.Buffers, am getting results like:
> >>
> >>
> >> rowBuff.get(1): 0 colBuff(1): 402653448 valBuff(1):
> 6.91730177312166E-310
> >>
> >>
> >> Have also tried reading into BytePointers similarly with the same type
> >> of results. I know that the use of Javacpp obfuscates what the problem
> >> may be. But I believe the Memorry is properly allocated.
> >>
> >>
> >>
> >> Sorry for the mistake.
> >>
> >>
> >> Thanks,
> >>
> >>
> >> Andy
> >>
> >>
> >> ------------------------------------------------------------------------
> >> *From:* Karl Rupp <r...@iue.tuwien.ac.at>
> >> *Sent:* Wednesday, July 20, 2016 3:50:07 PM
> >> *To:* Andrew Palumbo; ViennaCL-devel@lists.sourceforge.net
> >> *Subject:* Re: [ViennaCL-devel] Copying Values out of a
> compressed_matrix
> >> Hi Andy,
> >>
> >> instead of viennacl::backend::memory_copy(), you want to use
> >> viennacl::backend::memory_read(), which directly transfers the data into
> >> your buffer(s).
> >>
> >> If you *know* that your handles are in host memory, you can even grab
> >> the values directly via
> >> viennacl::linalg::host_based::detail::extract_raw_pointer<T>();
> >> defined in viennacl/linalg/host_based/common.hpp, around line 40.
> >>
> >> Please let me know if you still get errors after using that.
> >>
> >> Best regards,
> >> Karli
> >>
> >>
> >>
> >>
> >> On 07/20/2016 09:05 PM, Andrew Palumbo wrote:
> >>> Hello,
> >>>
> >>>
> >>> I'm Having some difficulties with compressed_matrix multiplication.
> >>>
> >>>
> >>> Essentially I am copying three buffers, the CSR conversion of an
> Apache
> >>> Mahout SparseMatrix, into two compressed_matrices performing matrix
> >>> multiplication. I am doing this in scala and Java using javacpp.
> >>>
> >>>
> >>> For example, I have a 5 x 10 matrix of ~20% non-zero values which in
> CSR
> >>> format looks like this:
> >>>
> >>>
> >>> NNz: 12
> >>>
> >>> Row Pointer: [0, 1, 4, 6, 9, 12, ]
> >>>
> >>> Col Pointer: [9, 0, 8, 7, 2, 9, 0, 8, 9, 0, 3, 5, ]
> >>>
> >>> element Pointer: [0.4065367203992265, 0.04957158909682802,
> >>> 0.5205586068847993, 0.3708618354358446, 0.6963900565931678,
> >>> 0.8330915529787706, 0.32839112750638844, 0.7856168903297948,
> >>> 0.4265801782090245, 0.14733066454561583, 0.9501663495824946,
> >>> 0.9710498974366047, ]
> >>>
> >>> Multiplied by a similarly Sparse 10 x 5 compressed_matrix
> >>>
> >>> I use a CompressedMatrix wrapper which essentially wraps the
> >>>
> >>> viennacl:: compressed_matrix (vcl_size_t rows, vcl_size_t cols,
> >>> vcl_size_t nonzeros=0, viennacl::context ctx=viennacl::context())
> >>>
> >>> constructor as well as the
> >>>
> >>> compressed_matrix (matrix_expression< const compressed_matrix,
> >>> const compressed_matrix, op_prod > const &proxy).
> >>>
> >>> I have a helper function, /toVclCompressedMatrix/(..) which essentially
> >>> does the CSR conversion from a Mahout src matrix, calls the constructor
> >>> and uses viennacl::compressed_matrix::set(...) to set the buffers:
> >>>
> >>> val ompA =toVclCompressedMatrix(src = mxA, ompCtx)
> >>> val ompB =toVclCompressedMatrix(src = mxB, ompCtx)
> >>>
> >>>
> >>> and then create a new viennacl::compressed_matrix from the
> >>> viennacl::linalg::prod of the 2 matrices i.e.:
> >>>
> >>> val ompC =new CompressedMatrix(prod(ompA, ompB))
> >>>
> >>> The context in the above case is either the Host or OpenMP (I know that
> >>> there is some special casting of the row_jumpers and col_idxs that
> needs
> >>> to be done in the OpenCL version)
> >>>
> >>> The Matrix multiplication completes without error on small Matrices eg.
> >>> < 300 x 300
> >>> but seems to overwrite the resulting buffers on larger Matrices.
> >>>
> >>> My real problem, though is getting the memory back out of the
> >>> resulting`ompC` compresed_matrix so that i can write it back to a
> mahout
> >>> SparseMatrix.
> >>>
> >>> currently I am using:
> >>>
> >>> void viennacl::backend::memory_copy (mem_handle const & src_buffer,
> >>> mem_handle & dst_buffer,
> >>> vcl_size_t src_offset,
> >>> vcl_size_t dst_offset,
> >>> vcl_size_t bytes_to_copy
> >>> )
> >>>
> >>> on ompC.handel1,ompC.handel2 and ompC.handel source handels
> >>>
> >>> to copy into pre-allocated row_jumper, col_index and element buffers
> >>> (of size ompC.size1() + 1, ompC.nnz and ompC.nnz, respectivly).
> >>>
> >>> I am getting nonsensical values back that one would expect from memory
> >>> errors. eg:
> >>>
> >>> the Matrix geometry of the result: ompC.size1(), and omp.size2() are
> >>> correct and ompC.nnz is a reasonable value.
> >>>
> >>> It is possible that I have mis-allocated some of the memory on my side,
> >>> but I am pretty sure that most of the Buffers are allocated correctly
> >>> (usually JavaCPP does a pretty good job of this).
> >>>
> >>>
> >>> I guess, long story short, my question is am i using the correct method
> >>> of copying the memory out of a compressed_matrix? is there something
> >>> glaringly incorrect that i am doing here? Should I be using
> >>> viennacl::backend::memory_copy or is there a different method that i
> >>> should be using?
> >>>
> >>>
> >>> Thanks very much,
> >>>
> >>> Andy
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
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> planning
> >>> reports.http://sdm.link/zohodev2dev
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> ViennaCL-devel mailing list
> >>> ViennaCL-devel@lists.sourceforge.net
> >>>https://lists.sourceforge.net/lists/listinfo/viennacl-devel
> >>>
> >>
> >
>
>
>
> ------------------------------------------------------------------------------
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>
>
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