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Update documentation
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@lan13005
lan13005 committed Nov 5, 2023
1 parent f507898 commit 5ce1c7a
Showing 9 changed files with 111 additions and 57 deletions.
2 changes: 1 addition & 1 deletion _sources/README.md
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@@ -8,4 +8,4 @@ Documentation is powered by jupyter-book (a distribution of sphinx). A makefile

`make update` - build and push

`make rebuild` - clean first then update
`make rebuild` - clean first then update
113 changes: 98 additions & 15 deletions _sources/notebooks/libraryLoading.ipynb
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@@ -16,9 +16,17 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 1,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Welcome to JupyROOT 6.28/06\n"
]
}
],
"source": [
"import os\n",
"import atiSetup\n",
@@ -34,22 +42,29 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"atiSetup| jupyter-lab called python3.9\n",
"\n",
"------------------------------------------------\n",
"atiSetup| MPI is disabled\n",
"atiSetup| GPU is disabled\n",
"------------------------------------------------\n",
"\n",
"\n",
"atiSetup| Loading library libAmpTools.so .............. ON\n",
"atiSetup| Loading library libAmpPlotter.so ............ ON\n",
"atiSetup| Loading library libAmpsDataIO.so ............ ON\n",
"atiSetup| Loading library libFSRoot.so ................ OFF\n",
"atiSetup| Loading library libAmpsGen.so ............... OFF\n",
"\n",
"\n",
"------------------------------------------------\n",
"MPI is disabled\n",
"GPU is disabled\n",
"Loading library libAmpTools.so .............. ON\n",
"Loading library libAmpPlotter.so ............ ON\n",
"Loading library libAmpsDataIO.so ............ ON\n",
"Loading library libFSRoot.so ................ OFF\n",
"Loading library libAmpsGen.so ............... OFF\n",
"------------------------------------------------\n",
"\n",
"Initializing AMPTOOLS_AMPS_DATAIO for PyROOT...\n"
@@ -58,7 +73,6 @@
],
"source": [
"############## SET ENVIRONMENT VARIABLES ##############\n",
"REPO_HOME = os.environ['REPO_HOME']\n",
"USE_MPI, USE_GPU, RANK_MPI = atiSetup.setup(globals()) # RANK_MPI defaults to 0 even if not using MPI"
]
},
@@ -71,12 +85,62 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"atiSetup| jupyter-lab called python3.9\n",
"\n",
"------------------------------------------------\n",
"atiSetup| MPI is disabled\n",
"atiSetup| GPU is disabled\n",
"------------------------------------------------\n",
"\n",
"\n",
"atiSetup| Loading library libAmpTools.so .............. ON\n",
"atiSetup| Loading library libAmpPlotter.so ............ ON\n",
"atiSetup| Loading library libAmpsDataIO.so ............ ON\n",
"atiSetup| Loading library libFSRoot.so ................ ON\n",
"atiSetup| Loading library libAmpsGen.so ............... ON\n",
"\n",
"\n",
"------------------------------------------------\n"
]
},
{
"ename": "AttributeError",
"evalue": "Failed to get attribute initialize_fsroot from ROOT",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m/home/lng/WORK/WORK/PyAmpTools/docs/notebooks/libraryLoading.ipynb Cell 7\u001b[0m line \u001b[0;36m2\n\u001b[1;32m <a href='vscode-notebook-cell://ssh-remote%2Bifarm/home/lng/WORK/WORK/PyAmpTools/docs/notebooks/libraryLoading.ipynb#W6sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0'>1</a>\u001b[0m \u001b[39m############## SET ENVIRONMENT VARIABLES ##############\u001b[39;00m\n\u001b[0;32m----> <a href='vscode-notebook-cell://ssh-remote%2Bifarm/home/lng/WORK/WORK/PyAmpTools/docs/notebooks/libraryLoading.ipynb#W6sdnNjb2RlLXJlbW90ZQ%3D%3D?line=1'>2</a>\u001b[0m USE_MPI, USE_GPU, RANK_MPI \u001b[39m=\u001b[39m atiSetup\u001b[39m.\u001b[39;49msetup(\u001b[39mglobals\u001b[39;49m(), use_fsroot\u001b[39m=\u001b[39;49m\u001b[39mTrue\u001b[39;49;00m, use_genamp\u001b[39m=\u001b[39;49m\u001b[39mTrue\u001b[39;49;00m) \u001b[39m# RANK_MPI defaults to 0 even if not using MPI\u001b[39;00m\n",
"File \u001b[0;32m/w/halld-scshelf2101/lng/Mambaforge/envs/PyAmpTools/lib/python3.9/site-packages/atiSetup.py:26\u001b[0m, in \u001b[0;36msetup\u001b[0;34m(calling_globals, accelerator, use_fsroot, use_genamp)\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39msetup\u001b[39m(calling_globals, accelerator\u001b[39m=\u001b[39m\u001b[39m'\u001b[39m\u001b[39mmpigpu\u001b[39m\u001b[39m'\u001b[39m, use_fsroot\u001b[39m=\u001b[39m\u001b[39mFalse\u001b[39;00m, use_genamp\u001b[39m=\u001b[39m\u001b[39mFalse\u001b[39;00m):\n\u001b[1;32m 17\u001b[0m \u001b[39m \u001b[39m\u001b[39m'''\u001b[39;00m\n\u001b[1;32m 18\u001b[0m \u001b[39m Performs basic setup, loading libraries and setting aliases\u001b[39;00m\n\u001b[1;32m 19\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 24\u001b[0m \u001b[39m use_genamp (bool): True if GenAmp library should be loaded\u001b[39;00m\n\u001b[1;32m 25\u001b[0m \u001b[39m '''\u001b[39;00m\n\u001b[0;32m---> 26\u001b[0m USE_MPI, USE_GPU, RANK_MPI \u001b[39m=\u001b[39m loadLibraries(accelerator, use_fsroot, use_genamp)\n\u001b[1;32m 27\u001b[0m set_aliases(calling_globals, USE_MPI)\n\u001b[1;32m 29\u001b[0m \u001b[39mreturn\u001b[39;00m USE_MPI, USE_GPU, RANK_MPI\n",
"File \u001b[0;32m/w/halld-scshelf2101/lng/Mambaforge/envs/PyAmpTools/lib/python3.9/site-packages/atiSetup.py:55\u001b[0m, in \u001b[0;36mloadLibraries\u001b[0;34m(accelerator, use_fsroot, use_genamp)\u001b[0m\n\u001b[1;32m 53\u001b[0m \u001b[39mif\u001b[39;00m RANK_MPI \u001b[39m==\u001b[39m \u001b[39m0\u001b[39m: \u001b[39mprint\u001b[39m(\u001b[39m\"\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39m\\n\u001b[39;00m\u001b[39m------------------------------------------------\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[1;32m 54\u001b[0m ROOT\u001b[39m.\u001b[39minitialize( RANK_MPI \u001b[39m==\u001b[39m \u001b[39m0\u001b[39m )\n\u001b[0;32m---> 55\u001b[0m \u001b[39mif\u001b[39;00m use_fsroot: ROOT\u001b[39m.\u001b[39;49minitialize_fsroot( RANK_MPI \u001b[39m==\u001b[39m \u001b[39m0\u001b[39m )\n\u001b[1;32m 56\u001b[0m \u001b[39mif\u001b[39;00m RANK_MPI \u001b[39m==\u001b[39m \u001b[39m0\u001b[39m: \u001b[39mprint\u001b[39m(\u001b[39m\"\u001b[39m\u001b[39m------------------------------------------------\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39m\"\u001b[39m)\n\u001b[1;32m 58\u001b[0m \u001b[39mreturn\u001b[39;00m USE_MPI, USE_GPU, RANK_MPI\n",
"File \u001b[0;32m/w/halld-scshelf2101/lng/WORK/PyAmpTools/root/root-6.28.06-gcc9.3.0/lib/ROOT/_facade.py:196\u001b[0m, in \u001b[0;36mROOTFacade._fallback_getattr\u001b[0;34m(self, name)\u001b[0m\n\u001b[1;32m 194\u001b[0m \u001b[39mif\u001b[39;00m res:\n\u001b[1;32m 195\u001b[0m \u001b[39mreturn\u001b[39;00m res\n\u001b[0;32m--> 196\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mAttributeError\u001b[39;00m(\u001b[39m\"\u001b[39m\u001b[39mFailed to get attribute \u001b[39m\u001b[39m{}\u001b[39;00m\u001b[39m from ROOT\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m.\u001b[39mformat(name))\n",
"\u001b[0;31mAttributeError\u001b[0m: Failed to get attribute initialize_fsroot from ROOT"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Initializing AMPTOOLS_AMPS_DATAIO for PyROOT...\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"cling::DynamicLibraryManager::loadLibrary(): /w/halld-scshelf2101/lng/WORK/PyAmpTools/external/FSRoot/lib/libFSRoot.so: undefined symbol: _ZTI17IncPiPiHistograms\n"
]
}
],
"source": [
"############## SET ENVIRONMENT VARIABLES ##############\n",
"REPO_HOME = os.environ['REPO_HOME']\n",
"USE_MPI, USE_GPU, RANK_MPI = atiSetup.setup(globals(), use_fsroot=True, use_genamp=True) # RANK_MPI defaults to 0 even if not using MPI"
]
},
@@ -89,7 +153,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -98,6 +162,13 @@
"TH1 = ROOT.TH1"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
@@ -111,6 +182,18 @@
"display_name": "PyAmpTools",
"language": "python",
"name": "pyamptools"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
}
},
"nbformat": 4,
12 changes: 0 additions & 12 deletions _sources/notebooks/mcmc.ipynb
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@@ -749,18 +749,6 @@
"display_name": "PyAmpTools",
"language": "python",
"name": "pyamptools"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
}
},
"nbformat": 4,
12 changes: 0 additions & 12 deletions _sources/notebooks/mle.ipynb
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@@ -455,18 +455,6 @@
"display_name": "PyAmpTools",
"language": "python",
"name": "pyamptools"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.18"
}
},
"nbformat": 4,
7 changes: 2 additions & 5 deletions notebooks/libraryLoading.html
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@@ -402,7 +402,6 @@ <h1>Loading Libraries<a class="headerlink" href="#loading-libraries" title="Perm
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1">############## SET ENVIRONMENT VARIABLES ##############</span>
<span class="n">REPO_HOME</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;REPO_HOME&#39;</span><span class="p">]</span>
<span class="n">USE_MPI</span><span class="p">,</span> <span class="n">USE_GPU</span><span class="p">,</span> <span class="n">RANK_MPI</span> <span class="o">=</span> <span class="n">atiSetup</span><span class="o">.</span><span class="n">setup</span><span class="p">(</span><span class="nb">globals</span><span class="p">())</span> <span class="c1"># RANK_MPI defaults to 0 even if not using MPI</span>
</pre></div>
</div>
@@ -438,7 +437,6 @@ <h1>Loading Libraries<a class="headerlink" href="#loading-libraries" title="Perm
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1">############## SET ENVIRONMENT VARIABLES ##############</span>
<span class="n">REPO_HOME</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;REPO_HOME&#39;</span><span class="p">]</span>
<span class="n">USE_MPI</span><span class="p">,</span> <span class="n">USE_GPU</span><span class="p">,</span> <span class="n">RANK_MPI</span> <span class="o">=</span> <span class="n">atiSetup</span><span class="o">.</span><span class="n">setup</span><span class="p">(</span><span class="nb">globals</span><span class="p">(),</span> <span class="n">use_fsroot</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">use_genamp</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> <span class="c1"># RANK_MPI defaults to 0 even if not using MPI</span>
</pre></div>
</div>
@@ -464,10 +462,9 @@ <h1>Loading Libraries<a class="headerlink" href="#loading-libraries" title="Perm
</div>
<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
<span class="ne">AttributeError</span><span class="g g-Whitespace"> </span>Traceback (most recent call last)
<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">line</span> <span class="mi">3</span>
<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">line</span> <span class="mi">2</span>
<span class="g g-Whitespace"> </span><span class="mi">1</span> <span class="c1">############## SET ENVIRONMENT VARIABLES ##############</span>
<span class="g g-Whitespace"> </span><span class="mi">2</span> <span class="n">REPO_HOME</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;REPO_HOME&#39;</span><span class="p">]</span>
<span class="ne">----&gt; </span><span class="mi">3</span> <span class="n">USE_MPI</span><span class="p">,</span> <span class="n">USE_GPU</span><span class="p">,</span> <span class="n">RANK_MPI</span> <span class="o">=</span> <span class="n">atiSetup</span><span class="o">.</span><span class="n">setup</span><span class="p">(</span><span class="nb">globals</span><span class="p">(),</span> <span class="n">use_fsroot</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">use_genamp</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> <span class="c1"># RANK_MPI defaults to 0 even if not using MPI</span>
<span class="ne">----&gt; </span><span class="mi">2</span> <span class="n">USE_MPI</span><span class="p">,</span> <span class="n">USE_GPU</span><span class="p">,</span> <span class="n">RANK_MPI</span> <span class="o">=</span> <span class="n">atiSetup</span><span class="o">.</span><span class="n">setup</span><span class="p">(</span><span class="nb">globals</span><span class="p">(),</span> <span class="n">use_fsroot</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">use_genamp</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> <span class="c1"># RANK_MPI defaults to 0 even if not using MPI</span>

<span class="nn">File /w/halld-scshelf2101/lng/Mambaforge/envs/PyAmpTools/lib/python3.9/site-packages/atiSetup.py:26,</span> in <span class="ni">setup</span><span class="nt">(calling_globals, accelerator, use_fsroot, use_genamp)</span>
<span class="g g-Whitespace"> </span><span class="mi">16</span> <span class="k">def</span> <span class="nf">setup</span><span class="p">(</span><span class="n">calling_globals</span><span class="p">,</span> <span class="n">accelerator</span><span class="o">=</span><span class="s1">&#39;mpigpu&#39;</span><span class="p">,</span> <span class="n">use_fsroot</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">use_genamp</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
4 changes: 2 additions & 2 deletions notebooks/mcmc.html
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@@ -871,7 +871,7 @@ <h1>Markov Chain Monte Carlo<a class="headerlink" href="#markov-chain-monte-carl
burnIn: 0
nsamples: 200
params_dict: {}
moves_mixture: [&lt;emcee.moves.stretch.StretchMove object at 0x7fb834135f70&gt;]
moves_mixture: [&lt;emcee.moves.stretch.StretchMove object at 0x7fe26179cf70&gt;]
sampler_kwargs: {&#39;progress&#39;: False}
===================================================================

@@ -896,7 +896,7 @@ <h1>Markov Chain Monte Carlo<a class="headerlink" href="#markov-chain-monte-carl
Re[resAmp3] = -193.365
Im[resAmp3] = 106.786
===============================================
Fit time: 9.378219604492188 seconds
Fit time: 9.754736423492432 seconds
Resetting source kin in /w/halld-scshelf2101/lng/WORK/PyAmpTools/tests/samples/SIMPLE_EXAMPLE/samples/data_generated_samples.root
</pre></div>
</div>
10 changes: 5 additions & 5 deletions notebooks/mle.html
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@@ -458,7 +458,7 @@ <h1>Maximum Likelihood Estimation<a class="headerlink" href="#maximum-likelihood
Config file: /w/halld-scshelf2101/lng/WORK/PyAmpTools/tests/samples/SIMPLE_EXAMPLE/fitInit.cfg
Seed file: seed_file
Number of random fits: 0
Random seed: 1699218615
Random seed: 1699226591
=============================
</pre></div>
</div>
@@ -689,10 +689,10 @@ <h1>Maximum Likelihood Estimation<a class="headerlink" href="#maximum-likelihood
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>LIKELIHOOD BEFORE MINIMIZATION: 112356.11732090596
LIKELIHOOD AFTER MINIMIZATION (NO RANDOMIZATION): 14346.408126566832
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>LIKELIHOOD AFTER MINIMIZATION (NO RANDOMIZATION): 14346.408126566832
Resetting source kin in /w/halld-scshelf2101/lng/WORK/PyAmpTools/tests/samples/SIMPLE_EXAMPLE/samples/data_generated_samples.root
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Resetting source kin in /w/halld-scshelf2101/lng/WORK/PyAmpTools/tests/samples/SIMPLE_EXAMPLE/samples/data_generated_samples.root

[ Minuit ]:

@@ -738,8 +738,8 @@ <h1>Maximum Likelihood Estimation<a class="headerlink" href="#maximum-likelihood

[ MinuitMinimizationManager ]:

MIGRAD evaluation total wall time: 2.60699e-01 s.
average time per function call: 8.63242e-01 ms.
MIGRAD evaluation total wall time: 2.60624e-01 s.
average time per function call: 8.62993e-01 ms.

[ NormIntInterface ]:

6 changes: 2 additions & 4 deletions reports/notebooks/libraryLoading.err.log
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@@ -16,7 +16,6 @@ Traceback (most recent call last):
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
############## SET ENVIRONMENT VARIABLES ##############
REPO_HOME = os.environ['REPO_HOME']
USE_MPI, USE_GPU, RANK_MPI = atiSetup.setup(globals(), use_fsroot=True, use_genamp=True) # RANK_MPI defaults to 0 even if not using MPI
------------------

@@ -45,10 +44,9 @@ cling::DynamicLibraryManager::loadLibrary(): /w/halld-scshelf2101/lng/WORK/PyAmp

---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[3], line 3
Cell In[3], line 2
 1 ############## SET ENVIRONMENT VARIABLES ##############
 2 REPO_HOME = os.environ['REPO_HOME']
----> 3 USE_MPI, USE_GPU, RANK_MPI = atiSetup.setup(globals(), use_fsroot=True, use_genamp=True) # RANK_MPI defaults to 0 even if not using MPI
----> 2 USE_MPI, USE_GPU, RANK_MPI = atiSetup.setup(globals(), use_fsroot=True, use_genamp=True) # RANK_MPI defaults to 0 even if not using MPI

File /w/halld-scshelf2101/lng/Mambaforge/envs/PyAmpTools/lib/python3.9/site-packages/atiSetup.py:26, in setup(calling_globals, accelerator, use_fsroot, use_genamp)
 16 def setup(calling_globals, accelerator='mpigpu', use_fsroot=False, use_genamp=False):
2 changes: 1 addition & 1 deletion searchindex.js
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