Yes. I'm going to check it in next week.
On Oct 14, 2014 12:44 AM, "Pablo Ródenas" <pablo.rodenas.bsc.es> wrote:
> Hi Scott,
>
> the execution is still running (it is a big input), but the process
> seems to be working as expected.
> Will be this change suitable for pmemd.cuda.MPI too?
>
> Cheers,
> Pablo.
>
>
> El 13/10/14 a las #4, Pablo Ródenas escribió:
> > Dear Scott,
> >
> > The execution of the last week finished successfully.
> >
> > I just recompile Amber with your files and the execution is running.
> > Let's see how it is going on.
> >
> > Best regards,
> > Pablo.
> >
> >
> >
> > El 10/10/14 a las #4, Scott Le Grand escribió:
> >> Sent you patch code off list to test out. If this works, I'll check it
> >> into the tree...
> >>
> >> Very minor changes...
> >>
> >>
> >> On Thu, Oct 9, 2014 at 11:36 PM, Pablo Ródenas <pablo.rodenas.bsc.es>
> wrote:
> >>
> >>> Good morning Scott,
> >>>
> >>> after modifying the code with your suggestions I get the following
> results:
> >>> with 255:
> >>> Error: unspecified launch failure launching kernel kClearForces
> >>> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
> >>>
> >>> with 256:
> >>> seems to be working.
> >>>
> >>> I will tell you how the executions ends.
> >>>
> >>> Thanks,
> >>> Pablo.
> >>>
> >>>
> >>> El 09/10/14 a las #4, Scott Le Grand escribió:
> >>>> You missed this part:
> >>>>
> >>>> unsigned int blocks = (gpu->sim.nfft1 * gpu->sim.nfft2 *
> gpu->sim.nfft3 +
> >>>> 255) >> 8;
> >>>>
> >>>>
> >>>>
> >>>> On Thu, Oct 9, 2014 at 8:54 AM, Pablo Ródenas <pablo.rodenas.bsc.es>
> >>> wrote:
> >>>>> Dear Scott,
> >>>>>
> >>>>> I tried with both changes:
> >>>>> kPMEReduceChargeGridBuffer_kernel<<<blocks, 255>>>();
> >>>>> and
> >>>>> kPMEReduceChargeGridBuffer_kernel<<<blocks, 256>>>();
> >>>>>
> >>>>> and the error arises again:
> >>>>> BLOCKS: 66150
> >>>>> NFFT: 360 196 120
> >>>>> Error: invalid configuration argument launching kernel
> >>>>> kPMEReduceChargeGridBuffer
> >>>>>
> >>>>> Is it there where I have to try with the values 255 and 256 for
> >>>>> ReduceChargeGridBuffer?
> >>>>>
> >>>>> Thanks,
> >>>>> Pablo.
> >>>>>
> >>>>> El 09/10/14 a las #4, Pablo Ródenas escribió:
> >>>>>> Hi Scott,
> >>>>>>
> >>>>>> the nfft values are respectively the followings:
> >>>>>> 360 196 120
> >>>>>>
> >>>>>> I just undo all my changes in ReduceChargeGridBuffer and I will try
> >>> with:
> >>>>>> kPMEReduceChargeGridBuffer_kernel<<<blocks, 255>>>();
> >>>>>> or
> >>>>>> kPMEReduceChargeGridBuffer_kernel<<<blocks, 256>>>();
> >>>>>>
> >>>>>> I will let you know any advance.
> >>>>>>
> >>>>>> Thank you very much.
> >>>>>>
> >>>>>> Best regards,
> >>>>>> Pablo.
> >>>>>>
> >>>>>>
> >>>>>> El 09/10/14 a las #4, Scott Le Grand escribió:
> >>>>>>> Also try 255 and 256 for ReduceChargeGridBuffer...
> >>>>>>>
> >>>>>>>
> >>>>>>> On Thu, Oct 9, 2014 at 8:23 AM, Scott Le Grand <
> varelse2005.gmail.com
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>> What is nfft1, nfft2, and nfft3 for this system?
> >>>>>>>>
> >>>>>>>> On Thu, Oct 9, 2014 at 8:20 AM, Pablo Ródenas <
> pablo.rodenas.bsc.es>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>> Dear Scott,
> >>>>>>>>>
> >>>>>>>>> you are right, this is a messy change.
> >>>>>>>>> We only saw clear to change from 65536 to 65535.
> >>>>>>>>> But after this change on the kPMEFillChargeGridBuffer function,
> we
> >>> got
> >>>>>>>>> the error on the kPMEReduceChargeGridBuffer one. We saw that the
> >>> value
> >>>>>>>>> of block variable on the kPMEReduceChargeGridBuffer function is
> >>> 66150,
> >>>>>>>>> greater than the one of our card, so we try to solve it with a
> quick
> >>>>>>>>> change in order to adapt it to our card maximum values. Please,
> >>> could
> >>>>>>>>> you try to fix this function too?
> >>>>>>>>>
> >>>>>>>>> FYI, the maximum values of our card are:
> >>>>>>>>> Maximum number of threads per block: 1024
> >>>>>>>>> Maximum sizes of each dimension of a block: 1024 x
> 1024 x
> >>> 64
> >>>>>>>>> Maximum sizes of each dimension of a grid: 65535 x
> 65535 x
> >>>>> 65535
> >>>>>>>>> Thank you very much for your answers!
> >>>>>>>>>
> >>>>>>>>> Best regards,
> >>>>>>>>> Pablo.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> El 09/10/14 a las #4, Scott Le Grand escribió:
> >>>>>>>>>> Also do *not* *mess* *with* LOADSIZE. You will wake the
> CUDAThuhlu
> >>>>> with
> >>>>>>>>>> such actions and no one wants that...
> >>>>>>>>>>
> >>>>>>>>>> The only change you should make here is changing 65536 to 65535.
> >>>>>>>>>>
> >>>>>>>>>> That said, thanks for hitting this corner case! Fix shortly...
> >>>>>>>>>>
> >>>>>>>>>> On Thu, Oct 9, 2014 at 8:06 AM, Scott Le Grand <
> >>>>> varelse2005.gmail.com>
> >>>>>>>>>> wrote:
> >>>>>>>>>>
> >>>>>>>>>>> Looking closer at this thread, could you try using 65,535
> instead
> >>> of
> >>>>>>>>>>> 65,536?
> >>>>>>>>>>>
> >>>>>>>>>>> http://en.wikipedia.org/wiki/CUDA, specifically maximum x
> >>> dimension
> >>>>>>>>> on SM
> >>>>>>>>>>> 2.0 GPUs is 65,535...
> >>>>>>>>>>>
> >>>>>>>>>>> Missed it by one... Works fine on any Kepler or better class
> GPU
> >>>>>>>>> because
> >>>>>>>>>>> this limit was raised to 2^31 - 1
> >>>>>>>>>>>
> >>>>>>>>>>> Ironically, y and z are still limited to 65,535. I'll check
> in a
> >>>>> fix
> >>>>>>>>>>> shortly...
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> On Thu, Oct 9, 2014 at 7:58 AM, Scott Le Grand <
> >>>>> varelse2005.gmail.com>
> >>>>>>>>>>> wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>> Broken.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Do not use this.
> >>>>>>>>>>>>
> >>>>>>>>>>>> The threadblocks *have* to be 64 for this to work (4 x 4 x 4
> >>>>>>>>>>>> interpolation)...
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> On Thu, Oct 9, 2014 at 7:22 AM, Pablo Ródenas <
> >>>>> pablo.rodenas.bsc.es>
> >>>>>>>>>>>> wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>>> Dear Jason and everybody,
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> finally I found that this Amber bug comes from the file
> >>>>>>>>>>>>> $AMBERHOME/src/pmemd/src/cuda/kPMEInterpolation.cu.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> There is the following hardcoded value (instead of getting
> it by
> >>>>>>>>> asking
> >>>>>>>>>>>>> to the card) in the function kPMEFillChargeGridBuffer which I
> >>>>>>>>> replaced
> >>>>>>>>>>>>> by the settings of my card (Tesla M2090):
> >>>>>>>>>>>>> + (line ~400)
> >>>>>>>>>>>>> int lblocks =
> >>> min(blocks,
> >>>>>>>>> 65535);
> >>>>>>>>>>>>> kPMEFillChargeGridBuffer_kernel<<<lblocks,
> >>>>> 64>>>(offset);
> >>>>>>>>>>>>> LAUNCHERROR("kPMEFillChargeGridBuffer");
> >>>>>>>>>>>>> offset +=
> 65535;
> >>>>>>>>>>>>> blocks -=
> 65535;
> >>>>>>>>>>>>> -
> >>>>>>>>>>>>> int lblocks =
> >>> min(blocks,
> >>>>>>>>> 65536);
> >>>>>>>>>>>>> kPMEFillChargeGridBuffer_kernel<<<lblocks,
> >>>>> 64>>>(offset);
> >>>>>>>>>>>>> LAUNCHERROR("kPMEFillChargeGridBuffer");
> >>>>>>>>>>>>> offset +=
> 65536;
> >>>>>>>>>>>>> blocks -=
> 65536;
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> After this change, Amber continues its execution until the
> next
> >>>>>>>>> error:
> >>>>>>>>>>>>> kPMEReduceChargeGridBuffer. I have also solved this error by
> >>>>>>>>> modifying
> >>>>>>>>>>>>> the function kPMEReduceChargeGridBuffer and its cuda kernel
> >>>>> function
> >>>>>>>>>>>>> kPMEReduceChargeGridBuffer_kernel. So my changes are:
> >>>>>>>>>>>>> + (line ~166)
> >>>>>>>>>>>>> kPMEReduceChargeGridBuffer_kernel(int offset)
> >>>>>>>>>>>>> {
> >>>>>>>>>>>>> unsigned int pos =
> >>> blockIdx.x *
> >>>>>>>>>>>>> blockDim.x + threadIdx.x + offset * blockDim.x;
> >>>>>>>>>>>>> -
> >>>>>>>>>>>>> kPMEReduceChargeGridBuffer_kernel()
> >>>>>>>>>>>>> {
> >>>>>>>>>>>>> unsigned int pos =
> >>> blockIdx.x *
> >>>>>>>>>>>>> blockDim.x + threadIdx.x;
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> and
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> + (line ~209)
> >>>>>>>>>>>>> long long blocks = (gpu->sim.nfft1 *
> gpu->sim.nfft2 *
> >>>>>>>>> gpu->sim.nfft3
> >>>>>>>>>>>>> + 127) >> 7;
> >>>>>>>>>>>>> int offset = 0;
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> while (blocks > 0)
> >>>>>>>>>>>>> {
> >>>>>>>>>>>>> long long lblocks
> =
> >>>>> min(blocks,
> >>>>>>>>>>>>> 65535ll);
> >>>>>>>>>>>>> kPMEReduceChargeGridBuffer_kernel<<<lblocks,
> >>>>>>>>> 128>>>(offset);
> >>>>>>>>>>>>> LAUNCHERROR("kPMEReduceChargeGridBuffer");
> >>>>>>>>>>>>> offset +=
> 65535;
> >>>>>>>>>>>>> blocks -=
> 65535;
> >>>>>>>>>>>>> }
> >>>>>>>>>>>>> -
> >>>>>>>>>>>>> unsigned int blocks = (gpu->sim.nfft1 *
> gpu->sim.nfft2 *
> >>>>>>>>>>>>> gpu->sim.nfft3 + 127) >> 7;
> >>>>>>>>>>>>> kPMEReduceChargeGridBuffer_kernel<<<blocks,
> 128>>>();
> >>>>>>>>>>>>> LAUNCHERROR("kPMEReduceChargeGridBuffer");
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Now it seems to work and I got 0 errors in the amber cuda
> tests.
> >>>>> But
> >>>>>>>>> I
> >>>>>>>>>>>>> cannot ensure that this code will produce the right values
> for
> >>> our
> >>>>>>>>>>>>> calculates, the execution is simply working.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Please, can you check your pmemd.cuda code in order to get it
> >>>>> working
> >>>>>>>>>>>>> for cards with lower grid and block size? Then we will be
> very
> >>>>> glad
> >>>>>>>>> if
> >>>>>>>>>>>>> you make a new update with a tested patch solving these
> issues.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Thank you for your attention.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Best regards,
> >>>>>>>>>>>>> Pablo.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> El 04/09/14 a las #4, Jason Swails escribió:
> >>>>>>>>>>>>>> On Thu, Sep 4, 2014 at 2:17 AM, Pablo Ródenas <
> >>>>> pablo.rodenas.bsc.es
> >>>>>>>>>>>>> wrote:
> >>>>>>>>>>>>>>> Good morning,
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> could you reproduce the problem with the files provided?
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>> O
> >>>>>>>>>>>>>> n my computer (GTX 680, 2 GB of memory), I get a memory
> >>>>> allocation
> >>>>>>>>>>>>> error
> >>>>>>>>>>>>>> because 2 GB is not enough for your system (ca. 700K+
> atoms).
> >>>>> When
> >>>>>>>>> I
> >>>>>>>>>>>>> move
> >>>>>>>>>>>>>> to a K20c (4 GB of memory), it runs fine for over 10 minutes
> >>>>> (after
> >>>>>>>>>>>>> which I
> >>>>>>>>>>>>>> killed it because your input files would have run for 10
> hours
> >>> on
> >>>>>>>>> the
> >>>>>>>>>>>>>> K20c). That machine has the nVidia toolkit version 5.0 and
> the
> >>>>>>>>> 331.38
> >>>>>>>>>>>>>> drivers on it.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> I'm not sure why you're having problems... Have you tried
> >>>>> running
> >>>>>>>>> the
> >>>>>>>>>>>>> GPU
> >>>>>>>>>>>>>> validation suite? I know Ross Walker posted a link to it
> on a
> >>>>>>>>> previous
> >>>>>>>>>>>>>> post, but I can't seem to locate it right now...
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> HTH,
> >>>>>>>>>>>>>> Jason
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> --
> >>>>>>>>>>>>> Pablo Ródenas Barquero (pablo.rodenas.bsc.es)
> >>>>>>>>>>>>> BSC - Centro Nacional de Supercomputación
> >>>>>>>>>>>>> C/ Jordi Girona, 31 WWW: http://www.bsc.es
> >>>>>>>>>>>>> 08034 Barcelona, Spain Tel: +34-93-405 42 29
> >>>>>>>>>>>>> e-mail: support.bsc.es Fax: +34-93-413 77 21
> >>>>>>>>>>>>> -----------------------------------------------
> >>>>>>>>>>>>> CNAG - Centre Nacional Anàlisi Genòmica
> >>>>>>>>>>>>> C/ Baldiri Reixac, 4 WWW: http://www.cnag.cat
> >>>>>>>>>>>>> 08028 Barcelona, Spain Tel: +34-93-403 37 54
> >>>>>>>>>>>>> e-mail: cnag_support.bsc.es
> >>>>>>>>>>>>> -----------------------------------------------
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> WARNING / LEGAL TEXT: This message is intended only for the
> use
> >>> of
> >>>>>>>>> the
> >>>>>>>>>>>>> individual or entity to which it is addressed and may contain
> >>>>>>>>>>>>> information which is privileged, confidential, proprietary,
> or
> >>>>> exempt
> >>>>>>>>>>>>> from disclosure under applicable law. If you are not the
> >>> intended
> >>>>>>>>>>>>> recipient or the person responsible for delivering the
> message
> >>> to
> >>>>> the
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> >>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>> AMBER mailing list
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> >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> AMBER mailing list
> >>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>> --
> >>>>>>>>> Pablo Ródenas Barquero (pablo.rodenas.bsc.es)
> >>>>>>>>> BSC - Centro Nacional de Supercomputación
> >>>>>>>>> C/ Jordi Girona, 31 WWW: http://www.bsc.es
> >>>>>>>>> 08034 Barcelona, Spain Tel: +34-93-405 42 29
> >>>>>>>>> e-mail: support.bsc.es Fax: +34-93-413 77 21
> >>>>>>>>> -----------------------------------------------
> >>>>>>>>> CNAG - Centre Nacional Anàlisi Genòmica
> >>>>>>>>> C/ Baldiri Reixac, 4 WWW: http://www.cnag.cat
> >>>>>>>>> 08028 Barcelona, Spain Tel: +34-93-403 37 54
> >>>>>>>>> e-mail: cnag_support.bsc.es
> >>>>>>>>> -----------------------------------------------
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> WARNING / LEGAL TEXT: This message is intended only for the use
> of
> >>> the
> >>>>>>>>> individual or entity to which it is addressed and may contain
> >>>>>>>>> information which is privileged, confidential, proprietary, or
> >>> exempt
> >>>>>>>>> from disclosure under applicable law. If you are not the intended
> >>>>>>>>> recipient or the person responsible for delivering the message to
> >>> the
> >>>>>>>>> intended recipient, you are strictly prohibited from disclosing,
> >>>>>>>>> distributing, copying, or in any way using this message. If you
> have
> >>>>>>>>> received this communication in error, please notify the sender
> and
> >>>>>>>>> destroy and delete any copies you may have received.
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> >>>>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>> --
> >>>>> Pablo Ródenas Barquero (pablo.rodenas.bsc.es)
> >>>>> BSC - Centro Nacional de Supercomputación
> >>>>> C/ Jordi Girona, 31 WWW: http://www.bsc.es
> >>>>> 08034 Barcelona, Spain Tel: +34-93-405 42 29
> >>>>> e-mail: support.bsc.es Fax: +34-93-413 77 21
> >>>>> -----------------------------------------------
> >>>>> CNAG - Centre Nacional Anàlisi Genòmica
> >>>>> C/ Baldiri Reixac, 4 WWW: http://www.cnag.cat
> >>>>> 08028 Barcelona, Spain Tel: +34-93-403 37 54
> >>>>> e-mail: cnag_support.bsc.es
> >>>>> -----------------------------------------------
> >>>>>
> >>>>>
> >>>>> WARNING / LEGAL TEXT: This message is intended only for the use of
> the
> >>>>> individual or entity to which it is addressed and may contain
> >>>>> information which is privileged, confidential, proprietary, or exempt
> >>>>> from disclosure under applicable law. If you are not the intended
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> >>>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
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> >>> --
> >>> Pablo Ródenas Barquero (pablo.rodenas.bsc.es)
> >>> BSC - Centro Nacional de Supercomputación
> >>> C/ Jordi Girona, 31 WWW: http://www.bsc.es
> >>> 08034 Barcelona, Spain Tel: +34-93-405 42 29
> >>> e-mail: support.bsc.es Fax: +34-93-413 77 21
> >>> -----------------------------------------------
> >>> CNAG - Centre Nacional Anàlisi Genòmica
> >>> C/ Baldiri Reixac, 4 WWW: http://www.cnag.cat
> >>> 08028 Barcelona, Spain Tel: +34-93-403 37 54
> >>> e-mail: cnag_support.bsc.es
> >>> -----------------------------------------------
> >>>
> >>>
> >>> WARNING / LEGAL TEXT: This message is intended only for the use of the
> >>> individual or entity to which it is addressed and may contain
> >>> information which is privileged, confidential, proprietary, or exempt
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> >>> received this communication in error, please notify the sender and
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> >>>
> >> _______________________________________________
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>
> --
> Pablo Ródenas Barquero (pablo.rodenas.bsc.es)
> BSC - Centro Nacional de Supercomputación
> C/ Jordi Girona, 31 WWW: http://www.bsc.es
> 08034 Barcelona, Spain Tel: +34-93-405 42 29
> e-mail: support.bsc.es Fax: +34-93-413 77 21
> -----------------------------------------------
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> C/ Baldiri Reixac, 4 WWW: http://www.cnag.cat
> 08028 Barcelona, Spain Tel: +34-93-403 37 54
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Received on Tue Oct 14 2014 - 07:00:02 PDT
