OpenLLM-France/wikimedia huggingface dataset:
# Parallel Spectral Numerical Methods/Finite Precision Arithmetic

For more on this see a text book on numerical methods such as Bradie. Because computers have a fixed amount of memory, floating point numbers can only be stored with a finite number of digits of precision. This limits the accuracy to which the solution to a numerical problem can be obtained in finite time. Most computers use binary IEEE 754 arithmetic to perform numerical calculations. There are other formats, but this will be the one of most relevance to us.

## Exercises

    1) Download the most recent IEEE 754 standard from http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=2355, see also http://grouper.ieee.org/groups/754/ -- unfortunately the links to the official standard require either IEEE membership or a subscription. If you do not have this please see the wikipedia page http://en.wikipedia.org/wiki/IEEE_754-2008 for the information you will need to answer the questions below. (These links are correct as of 1 April 2012, should they not be active, we expect that the information should be obtained by a search engine or by referring to a numerical analysis textbook such as Bradie.)
       a) In this standard what is the range of precision of numbers in:
             i) Single precision
             ii) Double precision
       b) What does the standard specify for quadruple precision?
       c) What does the standard specify about how elementary functions should be computed? How does this affect the portability of programs?
    2) Suppose we discretize a function for $x\in [-1,1]$. For what values of $\epsilon$ is
                   $\epsilon \log \left(\cosh \left({\frac {x}{\epsilon }}\right)\right)=\lVert x\rVert$
in:
       i) Single precision?
       ii) Double precision?
    3) Suppose we discretize a function for $x\in [-1,1]$. For what values of $\epsilon$ is
                   $\tanh \left({\frac {x}{\epsilon }}\right)={\begin{cases}1\quad x\geq 0\\-1\quad x<0\end{cases}}$
in:
       i) Single precision?
       ii) Double precision?
    4)
       a) What is the magnitude of the largest 4 byte integer in the IEEE 754 specification that can be stored?
       b) Suppose you are doing a simulation with $N^{3}$ grid points and need to calculate $N^{3}$. If $N$ is stored as a 4 byte integer, what is the largest value of $N$ for which $N^{3}$ can also be stored as a 4 byte integer?

## Notes

* ↑ Bradie (2006)
* ↑ Bradie (2006)

## References

Bradie, B. (2006). A Friendly Introduction to Numerical Analysis. Pearson.
http://en.wikibooks.org/wiki/Floating_Point
# GPU programs for Fourier pseudospectral simulations of the Navier-Stokes, Cubic Nonlinear Schrödinger and sine Gordon equations

This section includes the programs taken from a conference paper by Cloutier, Muite and Rigge. The main purpose is to give example programs which show how to use graphics processing units (GPUs) to solve partial differential equations using Fourier methods. For further background on GPUs and programming models for GPUs see Cloutier, Muite and Rigge. It should be noted that the algorithms used for the sine Gordon equation are very similar to those for the Klein Gordon equation discussed elsewhere in this tutorial. For consistency with the rest of the tutorial, only programs using CUDA Fortran and OpenACC extensions to Fortran are included although Cloutier, Muite and Rigge also has CUDA C programs. GPUs enable acceleration of Fourier pseudospectral codes by factors of 10 compared to OpenMP parallelizations on a single 8 core node.

## 2D Navier Stokes Equations

These programs use the Crank-Nicolson method.

## 2D Cubic Nonlinear Schrödinger Equations

These programs use splitting.

## 2D sine-Gordon Equations

These programs use a semi-explicit method that is similar to that used for the Klein-Gordon equation. Only the main program is included here, and the auxiliary subroutines can be downloaded from Cloutier, Muite and Rigge

## Notes

* ↑ Cloutier, Muite and Rigge (2012)
* ↑ Cloutier, Muite and Rigge (2012)
* ↑ Cloutier, Muite and Rigge (2012)
* ↑ Cloutier, Muite and Rigge (2012)

## References

B., Cloutier; B.K., Muite; P., Rigge. "Performance of FORTRAN and C GPU Extensions for a Benchmark Suite of Fourier Pseudospectral Algorithms". Proceedings of the Symposium on Application Accelerators in High Performance computing. IEEE. http://arxiv.org/abs/1206.3215.
# Parallel Spectral Numerical Methods/Gray Scott
## Background

${\frac {\partial u}{\partial t}}=D_{u}\nabla ^{2}u-uv^{2}+F(1-u)$
${\frac {\partial v}{\partial t}}=D_{v}\nabla ^{2}u+uv^{2}-(F+k)v$
The above reaction-diffusion system describes the density of two chemicals ,($u$ and $v$), reacting with another. First term in the equations is for the diffusion, the second describes the reaction of $u$ and $v$,($u+2v$ → $3v$) and the last term in the first equation is the input of new $u$, while in the second the last term removes $v$ from the system.

### Matlab Program

The program solves the linear part with fourier transformation and the nonlinear part with the implicit midpoint rule.
To compute the visualisation download vol3d.m.

### Fortran Program

The program uses 2decomp_fft like the programs from previous chapters.

### OpenCL

In OpenCL you write a 'Kernel' to do the intense work in parallel. You can choose to run the kernel on your cpu, gpu or some other coprocessor. The kernel is compiled during runtime for the device you have choosen.
To run the following code you need an valid OpenCL 1.2 framework for example AMD APP SDK which runs also on non AMD CPU's. You also need clfft an implementation of the FFT for OpenCL.
You can change "chooseplatform" and "choosedevice" to the device you want to compute on.
Now all the OpenCL-Kernel's, which should be saved in the same folder.
Here is your makefile! Change the clFFT to your path.
To run you need the INPUTFILE with the parameters.
* ↑ Information about the equations can be found at http://mrob.com/pub/comp/xmorphia/#formula.
* ↑ http://www.mathworks.com/matlabcentral/fileexchange/22940-vol3d-v2
* ↑ https://en.wikipedia.org/wiki/OpenCL
* ↑ http://developer.amd.com/tools-and-sdks/opencl-zone/amd-accelerated-parallel-processing-app-sdk/
* ↑ https://github.com/clMathLibraries/clFFT
# Pinyin/Port

A port is a place that has a harbor.
Gǎngkǒu shì yīgè yǒu hǎigǎng de dìfāng.
# Pinyin/Portugal

Search Pinyin Portugal
Portugal is a country in Southern Europe on the Iberian Peninsula. Portugal is the westernmost country of Europe. It is bordered by the Atlantic Ocean to the west and south, and by Spain to the north and east.
Portugal zaih Narn`ou d Iberia Bahndaao, shih Ouzhou zuih ximiahn d guorjia. ximiahn her narnmiahn xiangliarn Dahxi Yarng, beeimiahn her dongmiahn jieraang Spain.
Three groups of islands in the Atlantic Ocean are also part of Portugal: the Azores (Açores), Madeira and the Savage Isles (Ilhas Selvagens). The Savage Isles are a small group of islands with nobody on them, controlled by Madeira. Portugal claims that Olivença is also part of its territory, but actually it is controlled by Spain.
Dahxi Yarng d Azores, Madeira her Savage qurndaao yee shih Portugal d liingtuu. Savage Qurndaao shih yixie wurrern xiaaodaao, your Madeira guaanxiar. Portugal shengcheng Olivença yee shih ta d liingtuu, keeshih beih Spain shirjih kohngzhih.
# Pinyin/Possibility

See also
# Pinyin/Postpartum

See also
# Pinyin/Positive effect

See also
# Pinyin/Porcelain clay

See also
# Pinyin/Position

A position is the place that something is located.
Weihzhih shih mooushihwuh suoozaih de dihfang.
# Radiation Oncology/RTOG Trials/8307

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
RTOG 83-07 (PROSTATE)
* Title: Phase II Megestrol Acetate vs Diethylstilbestrol Adjuvant to Radiotherapy for Locally Advanced Stage B/C Carcinoma of the Prostate
* Objectives:
** (1) Evaluate the relative effectiveness and toxicity of megestrol acetate versus diethylstilbestrol as pre-adjuvants to radiotherapy; the principal endpoints are tumor clearance rates and serum testosterone levels.
** (2) Compare the two treatment options with respect to local-regional control, disease-free interval, and survival.
** (3) Assess the effect of both treatments on sexual function.
* Protocol
** Arm 1: Megestrol x 2 months followed by 65-70 Gy EBRT + Megestrol
** Arm 2: Diethylstilbestrol x 2 months followed by 65-70 Gy EBRT + Diethylstilbestrol
* Eligibility: Stage B2 or C, LN+ ok if below aortic bifurcation, M0
* Enrolled: 203 patients
* Conclusion:
** PMID 7721614 -- Phase II trial of hormonal cytoreduction with megestrol and diethylstilbestrol in conjunction with radiotherapy for carcinoma of the prostate: outcome results of RTOG 83-07. (Pilepich MV, IJRBOP 1995). Conclusion: The results of the study indicate comparable efficacy (using tumor clearance as an end point) of DES and Megestrol. Although DES appears more effective in suppressing testosterone, it is also associated with a higher incidence of drug-related toxicity.
* Publications:
** PMID 10837944 -- Predicting long-term survival, and the need for hormonal therapy: a meta-analysis of RTOG prostate cancer trials. (Roach M, IJRBOP 2000). Conclusion: Based on this meta-analysis of RTOG trials, subsets of patients can be identified who either do not appear to benefit from the use of hormonal therapy, benefit from short-term hormonal therapy, or who benefit only from long-term hormonal therapy. These observations should be confirmed by prospective randomized trials before they can be considered conclusive. In the meantime, however, these observations provide rational guidelines for deciding who should receive hormonal therapy and for how long.
** PMID 7591889 -- Correlation of survival with quantitative tissue staining of prostate specific acid phosphatase in patients with prostate carcinoma by using microscopic image analysis: a preliminary report of correlative studies on RTOG protocols 75-06, 77-06, and 83-07. (Zhou R, IJRBOP 1995). Conclusion: Quantitative image analysis of the IPSAP stain predicts survival in patients treated with external beam radiotherapy with and without prior hormonal therapy.
** PMID 2646266 -- Hormonal cytoreduction in locally advanced carcinoma of the prostate treated with definitive radiotherapy: preliminary results of RTOG 83-07. (Pilepich MV, IJRBOP 1989). Conclusion: The results of the study indicate comparable efficacy (using tumor clearance as an end-point) of DES and Megestrol. While DES appears more effective in suppressing testosterone it is also associated with a higher incidence of toxicity. The cytoreduction (using either DES, Megestrol, or an alternative regimen) concept remains to be tested in a Phase III study comparing it to radiotherapy alone.
# Radiation Oncology/RTOG Trials/8519

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
RTOG 85-19 (PROSTATE)
* Title: Phase II (title not available)
* Objectives: (not available)
* Protocol: (not available)
* Eligibility: Bulky primary lesions, stage B2 and C, with disease confined to the pelvis
* Enrolled: 31 patients
* Conclusion:
** PMID 2146872 -- Phase II Radiation Therapy Oncology Group study of hormonal cytoreduction with flutamide and Zoladex in locally advanced carcinoma of the prostate treated with definitive radiotherapy. (Pilepich MV, Am J Clin Oncol 1990). Conclusion: The observed toxicity appears acceptable and the response rate encouraging.
# Radiation Oncology/RTOG Trials/7928

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
RTOG 79-28 (LIVER)
* Title: Phase I-II Study of Combined Modality Treatment of Primary Liver Cancer with Isotopic Immunoglobulin, Liver Irradiation, and ADR/5-FU
* Objective:
** I. Determine the therapeutic efficacy of combining administration of radiolabeled anti-CEA or anti-ferritin with whole liver radiotherapy plus combination chemotherapy using adriamycin/5-fluorouracil in patients with primary liver cancer.
** II. Determine the maximal tolerated dose of radiolabeled antibody and the toxicities associated with this treatment.
** III. Determine the dose distributions of anti-CEA and anti-ferritin in the tumor and in the entire body and compare the dose distributions of the 2 antibodies in hepatoma.
* Protocol:
** Nonrandomized study. Following treatment on Regimens A and B, patients with hepatic biliary carcinoma are entered to Arm I and patients with hepatoma to Arm I or Arm II.
** Regimen A: Adriamycin/5-FU + whole liver RT
** Regimen B: Adriamycin/5-FU
** Arm I: I-131-labeled anti-CEA.
** Arm II: I-131-labeled anti-ferritin.
** Maintenance: Adriamycin/5-FU
* Eligibility: Histologically documented primary hepatic malignancy who have measurable or evaluable disease.
* Enrolled:
* Conclusion:
** PMID 6275989 -- Phase I-II study of isotopic immunoglobulin therapy for primary liver cancer. (Ettinger DS, Cancer Treat Rep. 1982 Feb;66(2):289-97.) Conclusion: "Present results suggest that further clinical studies with isotopic immunoglobulin are indicated."
* Publications:
** PMID 2998178 -- Computed tomography assisted volumetric analysis of primary liver tumor as a measure of response to therapy. (Ettinger DS, Am J Clin Oncol. 1985 Oct;8(5):413-8.) Conclusion: "In spite of small changes in total liver volume, there may be concomitantly substantial changes in tumor volume.
** PMID 6085756 -- Comparative tumor dose from 131I-labeled polyclonal anti-ferritin, anti-AFP, and anti-CEA in primary liver cancers. (Leichner PK, Cancer Drug Deliv. 1984 Fall;1(4):321-8.)
** PMID 6307515 -- Dosimetry of 131I-labeled antiferritin in hepatoma: specific activities in the tumor and liver. (Leichner PK, Cancer Treat Rep. 1983 Jul-Aug;67(7-8):647-58.) Conclusion: "These data, in conjunction with toxicity studies and tumor effective half-life measurements, led to the present treatment regimen of administering 30 mCi of polyclonal antiferritin IgG on Day 0 and 20 mCi on Day 5 following the first injection."
** PMID 6275989 -- Phase I-II study of isotopic immunoglobulin therapy for primary liver cancer. (Ettinger DS, Cancer Treat Rep. 1982 Feb;66(2):289-97.) Conclusion: "Present results suggest that further clinical studies with isotopic immunoglobulin are indicated."
** PMID 6268576 -- Dosimetry of 131I-labeled anti-ferritin in hepatoma: a model for radioimmunoglobulin dosimetry. (Leichner PK, Int J Radiat Oncol Biol Phys. 1981 Mar;7(3):323-33.)
# Radiation Oncology/RTOG Trials/8405

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
RTOG 84-05 (LIVER)
* Title: Phase I/II Dose-Escalating Trial of Accelerated Fractionation in the Palliative Irradiation of Hepatic Metastases from Primary Cancer of the GI Tract
* Objective:
** I. Assess the feasibility and efficacy of a twice-daily schedule of radiation treatments in the palliation of patients with liver metastases from cancer of the stomach, pancreas, gallbladder, biliary tree, colon, or rectum.
** II. Determine whether greater doses of hepatic irradiation in a selected population of prognostically favorable patients can result in a decreasing frequency of progressive liver metastases as a direct cause of death.
** III. Help define the tolerance of the liver to fractionated irradiation delivered in dose fractions that may ultimately be clinically useful in the elective or adjuvant irradiation of the liver in high-risk patients with primary cancers draining via the portal circulation.
* Protocol: Whole liver dose escalation 27 Gy -> 36 Gy given in 1.5 Gy/fx BID
* Eligibility: Measurable hepatic metastases (as documented by CT scan) from histologically verified primary cancers arising in the stomach, pancreas, gallbladder, biliary tree, colon, or rectum. All cell types are permissible except leukemia, plasmacytoma, and lymphoma.
* Enrolled: 173 patients
* Conclusion:
** PMID 8365932 -- Accelerated hyperfractionated hepatic irradiation in the management of patients with liver metastases: results of the RTOG dose escalating protocol. (Russel AH, Int J Radiat Oncol Biol Phys. 1993 Sep 1;27(1):117-23.) Conclusion: "The study design could not credibly establish a safe dose for hepatic irradiation, however, it did succeed in determining that 33 Gy in fractions of 1.5 Gy is unsafe, carrying a substantial risk of delayed radiation injury. The absence of apparent late liver injury at the 27 Gy and 30 Gy dose levels suggests that a prior clinical trial of adjuvant hepatic irradiation in patients with resected colon cancer may have employed an insufficient radiation dose (21 Gy) to fully test the question."
* Publications:
# Radiation Oncology/RTOG Trials/7810

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
RTOG 78-10 (PALLIATION)
* Title: Phase I/II Study of Half-Body Radiotherapy for Multiple Osseous Metastases
* Objectives:
** (1) Evaluate the frequency and the duration of pain relief as a function of the dose schedules proposed.
** (2) Assess tumor and response by evaluation of measurable lesions in different sites.
** (3) Determine the normal tissue tolerance and toxicity following single exposure doses of irradiation, particularly focusing on the dose-limiting organs: bone marrow, lung, kidney, liver, brain, spinal cord, small bowel and heart, both in terms of acute and late reactions and damage.
** (4) Study the natural history of progression of disseminated cancer, particularly the osseous lesions, and develop a useful staging system for evaluation of disseminated disease.
* NCI_Protocol: Dose escalation of hemibody irradiation
* Enrolled: 168 patients
* Conclusion:
** PMID 2423225 -- Single-dose half-body irradiation for palliation of multiple bone metastases from solid tumors. Final Radiation Therapy Oncology Group report. (Salazar OM, Cancer 1986). Conclusion: "HBI achieves pain relief sooner and with less evidence of pain recurrence in the irradiated area than conventionally treated patients. The most effective and safest of the HBI doses tested were 600 rad for the upper HBI and 800 rad for the lower or mid-HBI."
* Publications:
** PMID 6178497 -- The palliation of symptomatic osseous metastases: final results of the Study by the Radiation Therapy Oncology Group. (Tong D, Cancer 1982). Review.
** PMID 6169699 -- Single-dose half-body irradiation for the palliation of multiple bone metastases from solid tumors: a preliminary report. (Salazar OM, IJRBOP 1981). No abstract.
# Radiation Oncology/RTOG Trials/8003

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
RTOG 80-03 (LIVER)
* Title: Phase III Comparison of Radiation Alone vs Radiation plus Misonidazole in the Treatment of Liver Metastases
* Objective:
** I. Compare the frequency and duration of symptomatic relief in patients with liver metastases from a variety of sites treated by radiotherapy alone vs. radiotherapy plus misonidazole.
** II. Compare the frequency and duration of normalization of liver function in these 2 groups.
** III. Compare the frequency of decrease in the size of liver metastases by CT scans in the 2 groups.
** IV. Evaluate the response for each treatment according to site and histology of the primary, performance status, and tumor volume.
** V. Evaluate the foregoing objective with respect to the length of survival.
* Protocol:
** Arm 1: RT (whole liver to a dose of 21.0 Gy in 3 Gy/fx)
** Arm 2: RT + radiosensitization with Misonidazole
* Eligibility: Patients with histologic verification of malignancy other than leukemia, myeloma, or lymphoma, and with hepatic metastases as documented by liver scan and/or CT scan.
* Enrolled: 214 patients
* Conclusion:
** PMID 3597149 -- A comparison of misonidazole sensitized radiation therapy to radiation therapy alone for the palliation of hepatic metastases: results of a Radiation Therapy Oncology Group randomized prospective trial. (Leibel SA, Int J Radiat Oncol Biol Phys. 1987 Jul;13(7):1057-64.) Conclusion: "The addition of misonidazole did not significantly improve the therapeutic response to radiation therapy in any of the parameters studied."
* Publications:
** PMID 2180867 -- Accelerated fractionation radiation therapy for liver metastases: selection of an optimal patient population for the evaluation of late hepatic injury in RTOG studies. (Leibel SA, Int J Radiat Oncol Biol Phys. 1990 Mar;18(3):523-8. Conclusion: Favorable characteristics: KPS >=80, CRC primary, no extrahepatic mets
# Radiation Oncology/RTOG Trials/8301

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
RTOG 83-01 (LIVER)
* Title: Phase I/II evaluation of I-131 Antiferritin after RT/CT induction
* Objective:
** I. Provide the necessary data to determine the maximum safe dose of adriamycin and 5-fluorouracil that can be combined with I-131 antiferritin IgG (given 30 mCi on day 0 and 20 mCi on day 5).
** II. Determine whether 20 mCi I-131 anti-AFP plus 30 mCi antiferritin increases tumor dose deposition and offers advantage in tumor effective half-life and dose deposition over I-131 antiferritin alone.
** III. Combine the radiolabeled preparation considered best (on dosimetric grounds) with escalating doses of adriamycin and 5-fluorouracil.
** IV. Determine the best combination of adriamycin and 5-fluorouracil plus I-131 labeled antibody for Phase II trial in AFP and non-AFP hepatomas.
** V. Complete Phase II trials using physical exam and CT tumor volume reconstruction to determine the remission rate, duration of remission, and survival.
* Protocol:
** Induction RT (21.0 Gy at 3.0 Gy/Fx or 24.0 Gy at 1.5 Gy/Fx BID) + low-dose CT (5-FU/adriamycin)
** 1 month later I-131-antiferritin + 5-FU/adriamycin
* Eligibility: histologically confirmed primary hepatic malignancy
* Enrolled: 216 patients
* Conclusion:
** PMID 2415692 -- Iodine 131 antiferritin, a new treatment modality in hepatoma: a Radiation Therapy Oncology Group study. (Order SE, J Clin Oncol. 1985 Dec;3(12):1573-82.) Conclusion: "These studies have demonstrated the toxicity and therapeutic activity of 131I antiferritin and the emerging role of radiolabelled antibody in cancer therapy."
* Publications:
** PMID 1850722 -- A randomized prospective trial comparing full dose chemotherapy to 131I antiferritin: an RTOG study. (1991 Order S, Int J Radiat Oncol Biol Phys. 1991 May;20(5):953-63.) Conclusion: "Overall, radiolabeled antibody administration and full dose chemotherapy led to equivalent partial remission rates (22-30% vs 23-25%) and survival rates compared to chemotherapy (6 month median; AFP+ 5 months; AFP- 10 months)."
** PMID 1847127 -- Prognostic factors in unresectable hepatocellular cancer: Radiation Therapy Oncology Group Study 83-01. (Stillwagon GB, Int J Radiat Oncol Biol Phys. 1991 Jan;20(1):65-71.) Conclusion: "Good and poor prognostic groups were defined and compared to a similar patient population (RTOG study 83-19) with confirmation of the validity of the model"
** PMID 2998178 -- Computed tomography assisted volumetric analysis of primary liver tumor as a measure of response to therapy. (Ettinger DS, Am J Clin Oncol. 1985 Oct;8(5):413-8.) Conclusion: "In spite of small changes in total liver volume, there may be concomitantly substantial changes in tumor volume.
** PMID 6085756 -- Comparative tumor dose from 131I-labeled polyclonal anti-ferritin, anti-AFP, and anti-CEA in primary liver cancers. (Leichner PK, Cancer Drug Deliv. 1984 Fall;1(4):321-8.) Conclusion: "Polyclonal anti-ferritin has, therefore, become the antibody of choice in the treatment of hepatoma."