Changeset aa8c6e0 in sasmodels for doc/guide

Timestamp:

Oct 30, 2018 8:43:35 AM (6 years ago)

Author:

Paul Kienzle <pkienzle@…>

Branches:

master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

765d025, 23df833

Parents:

153f8f6 (diff), c6084f1 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'master' into beta_approx

Location:

doc/guide

Files:

• plugin.rst (modified) (5 diffs)
• gpu_setup.rst (modified) (4 diffs)

doc/guide/plugin.rst

@@ -744 +744 @@
     erf, erfc, tgamma, lgamma:  **do not use**
         Special functions that should be part of the standard, but are missing
-        or inaccurate on some platforms. Use sas_erf, sas_erfc and sas_gamma
-        instead (see below). Note: lgamma(x) has not yet been tested.
+        or inaccurate on some platforms. Use sas_erf, sas_erfc, sas_gamma
+        and sas_lgamma instead (see below).
 
 Some non-standard constants and functions are also provided:
@@ -812 +812 @@
         Gamma function sas_gamma\ $(x) = \Gamma(x)$.
 
-        The standard math function, tgamma(x) is unstable for $x < 1$
+        The standard math function, tgamma(x), is unstable for $x < 1$
         on some platforms.
 
         :code:`source = ["lib/sas_gamma.c", ...]`
         (`sas_gamma.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gamma.c>`_)
+
+    sas_gammaln(x):
+        log gamma function sas_gammaln\ $(x) = \log \Gamma(|x|)$.
+
+        The standard math function, lgamma(x), is incorrect for single
+        precision on some platforms.
+
+        :code:`source = ["lib/sas_gammainc.c", ...]`
+        (`sas_gammainc.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gammainc.c>`_)
+
+    sas_gammainc(a, x), sas_gammaincc(a, x):
+        Incomplete gamma function
+        sas_gammainc\ $(a, x) = \int_0^x t^{a-1}e^{-t}\,dt / \Gamma(a)$
+        and complementary incomplete gamma function
+        sas_gammaincc\ $(a, x) = \int_x^\infty t^{a-1}e^{-t}\,dt / \Gamma(a)$
+
+        :code:`source = ["lib/sas_gammainc.c", ...]`
+        (`sas_gammainc.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gammainc.c>`_)
 
     sas_erf(x), sas_erfc(x):
@@ -854 +872 @@
         If $n$ = 0 or 1, it uses sas_J0($x$) or sas_J1($x$), respectively.
 
+        Warning: JN(n,x) can be very inaccurate (0.1%) for x not in [0.1, 100].
+
         The standard math function jn(n, x) is not available on all platforms.
 
@@ -862 +882 @@
         Sine integral Si\ $(x) = \int_0^x \tfrac{\sin t}{t}\,dt$.
 
+        Warning: Si(x) can be very inaccurate (0.1%) for x in [0.1, 100].
+
         This function uses Taylor series for small and large arguments:
 
-        For large arguments,
+        For large arguments use the following Taylor series,
 
         .. math::
@@ -872 +894 @@
              - \frac{\sin(x)}{x}\left(\frac{1}{x} - \frac{3!}{x^3} + \frac{5!}{x^5} - \frac{7!}{x^7}\right)
 
-        For small arguments,
+        For small arguments ,
 
         .. math::

doc/guide/gpu_setup.rst

@@ -94 +94 @@
 Device Selection
 ================
+**OpenCL drivers**
+
 If you have multiple GPU devices you can tell the program which device to use.
 By default, the program looks for one GPU and one CPU device from available
@@ -104 +106 @@
 was used to run the model.
 
-**If you don't want to use OpenCL, you can set** *SAS_OPENCL=None*
-**in your environment settings, and it will only use normal programs.**
-
-If you want to use one of the other devices, you can run the following
+If you want to use a specific driver and devices, you can run the following
 from the python console::
 
@@ -115 +114 @@
 This will provide a menu of different OpenCL drivers available.
 When one is selected, it will say "set PYOPENCL_CTX=..."
-Use that value as the value of *SAS_OPENCL*.
+Use that value as the value of *SAS_OPENCL=driver:device*.
+
+To use the default OpenCL device (rather than CUDA or None),
+set *SAS_OPENCL=opencl*.
+
+In batch queues, you may need to set *XDG_CACHE_HOME=~/.cache* 
+(Linux only) to a different directory, depending on how the filesystem 
+is configured.  You should also set *SAS_DLL_PATH* for CPU-only modules.
+
+    -DSAS_MODELPATH=path sets directory containing custom models
+    -DSAS_OPENCL=vendor:device|cuda:device|none sets the target GPU device
+    -DXDG_CACHE_HOME=~/.cache sets the pyopencl cache root (linux only)
+    -DSAS_COMPILER=tinycc|msvc|mingw|unix sets the DLL compiler
+    -DSAS_OPENMP=1 turns on OpenMP for the DLLs
+    -DSAS_DLL_PATH=path sets the path to the compiled modules
+
+
+**CUDA drivers**
+
+If OpenCL drivers are not available on your system, but NVidia CUDA
+drivers are available, then set *SAS_OPENCL=cuda* or
+*SAS_OPENCL=cuda:n* for a particular device number *n*.  If no device
+number is specified, then the CUDA drivers looks for look for
+*CUDA_DEVICE=n* or a file ~/.cuda-device containing n for the device number.
+
+In batch queues, the SLURM command *sbatch --gres=gpu:1 ...* will set
+*CUDA_VISIBLE_DEVICES=n*, which ought to set the correct device
+number for *SAS_OPENCL=cuda*.  If not, then set
+*CUDA_DEVICE=$CUDA_VISIBLE_DEVICES* within the batch script.  You may
+need to set the CUDA cache directory to a folder accessible across the
+cluster with *PYCUDA_CACHE_DIR* (or *PYCUDA_DISABLE_CACHE* to disable
+caching), and you may need to set environment specific compiler flags
+with *PYCUDA_DEFAULT_NVCC_FLAGS*.  You should also set *SAS_DLL_PATH* 
+for CPU-only modules.
+
+**No GPU support**
+
+If you don't want to use OpenCL or CUDA, you can set *SAS_OPENCL=None*
+in your environment settings, and it will only use normal programs.
+
+In batch queues, you may need to set *SAS_DLL_PATH* to a directory
+accessible on the compute node.
+
 
 Device Testing
@@ -154 +195 @@
 *Document History*
 
-| 2017-09-27 Paul Kienzle
+| 2018-10-15 Paul Kienzle