Sumber Belajar

Bacaan Ringan

1. Alternatif baru dalam pengobatan kanker, http://kankerpayudara.wordpress.com/2008/08/01/alternatif-baru-dalam-pengobatan-kanker/
2. How We Use Photodynamic Therapy (PDT) to Defeat Skin  Cancer, http://akronmohs.com/dsc/how-we-use-photodynamic-therapy-pdt-to-defeat-skin-cancer/
3. Penanggulangan Kanker di Indonesia : Peran Nanotechnology dalam Diagnosis dan Terapi (Cholid Badri), http://jusami.batan.go.id/dokumen/materi/30Jan12_134429_Ckolid%20Badri.pdf
4. Cluster Neoplasma pada program S3 Fakultas Kedokteran UGM,  Photodynamic Therapy (PDT)  menjadi salah satu agenda risetnya, http://clusters3.fk.ugm.ac.id/cluster/7
5. Tentang Fuda Cancer Hospital, Photodynamic Therapy (PDT)  adalah salah satu metode yang digunakan di rumah sakit ini, http://fudaindonesia.com/about-us/

Publikasi Ilmiah 

1. Perkembangan sensitizer pada terapi fotodinamika tumor dan kanker hingga penuntunan nanopartikel (nanoparticulate targetting) dengan antibodi monoklonal, http://ris.uksw.edu/jurnal/read/kode/j00350
2. TIM-OS: A General Monte Carlo Optical Simulator for Biomedical Optics, https://sites.google.com/a/imaging.sbes.vt.edu/tim-os/

Buku

1. Parallel Programming with Intel Parallel Studio XE, http://astore.amazon.com/photodynamic-therapy-20/detail/0470891653

Tools

1. Intel® Parallel Studio XE, https://software.intel.com/en-us/intel-education-offerings#pid-2460-93
• Using Intel® C++ Compiler with the Eclipse* IDE on Linux*, https://software.intel.com/en-us/articles/intel-c-compiler-for-linux-using-intel-compilers-with-the-eclipse-ide-pdf 
2. Download Visual Studio Community & Express, http://www.visualstudio.com/en-us/downloads/download-visual-studio-vs#DownloadFamilies_2   - Catatan : Visual Studio Communiy & Express tidak bisa diintegrasikan secara penuh dengan Intel Parallel Studi Express, kita tidak bisa melakukan kompilasi dengan Intel Compiler dengan Visual Studio Community Edition. Anda harus menggunakan Visual Studio Ultimate. 
• Using other libraries in Visual C++ 2012, http://stackoverflow.com/questions/13637462/using-other-libraries-in-visual-c-2012
3. Eclipse, http://www.eclipse.org/downloads/?

Kompilasi TIM-OS: A General Monte Carlo Optical Simulator for Biomedical Optics

Windows : Visual Studio dengan Intel C++ Compiler

Ketika kompilasi, salah satu issue yang didapat adalah tidak dapat meng-include pthread.h, pthread.h dapat didapatkan di [1].

Sesudah masalah pthread.h beres, tinggal mengedit Additional IncludeDirectories untuk memasukkan header-header MKL (Math Kernel Library).

Entri nya menjadi :

C:\Program Files (x86)\Intel\Composer XE 2015\mkl\include;D:\software\pthreads-w32-2-9-1-release\Pre-built.2\include;%

Masalah utama sekarang adalah, ada beberapa header yang tidak terdapat di windows, yaitu :

sys/sysinfo.h ,  sys/systime.h, sys/resource.h

Berikut error lengkap ketika proses kompilasi :

Instalasi Intel(R) Parallel Studio XE di WIndows

OS :  Windows 7 Home, Intel(R) Core (T) i5-2430M @2.40GHz  2.40 GHz
System type : 64-bit Operating System

 Ketika proses instalasi, installer memberitahu ada beberapa prasyarat yang belum terpenuhi :

System reboot may be required.
To collect extended data for workloads running on Intel(R) Integrated Graphics, make sure to reboot the system before analysis.

 The Intel(R) Debugger Extension for Intel(R) MIC Architecture cannot be installed.
Installation can continue; however, Intel(R) Debugger Extension for Intel(R) MIC Architecture will not be installed because it requires that Microsoft Visual Studio* 2012 or 2013 be installed. Refer to the Release Notes for more details.

 Microsoft Visual Studio 2010* Shell is available for installing from this package.
Please note that Visual Studio Shell does not support use of Intel C++ Compiler XE – it is for use with Intel Visual Fortran Compiler XE only.

Installation Summary :

Intel Parallel Studio XE 2015 Update 1 Professional Edition for C++
Destination Folder(s):
   C:\Program Files (x86)\Intel\Parallel Studio XE 2015
   C:\Program Files (x86)\Intel
   C:\Program Files (x86)\Intel\Composer XE 2015
   C:\Program Files (x86)\Intel\VTune Amplifier XE 2015
   C:\Program Files (x86)\Intel\Inspector XE 2015
   C:\Program Files (x86)\Intel\Advisor XE 2015
Following components will be installed:
       Intel C++ Compiler XE 15.0 Update 1
          Intel C++ Compiler XE for IA-32
          Intel C++ Compiler XE for Intel® 64
       Intel Math Kernel Library 11.2 Update 1
          Intel MKL core libraries for Intel® 64
          Fortran 95 interfaces for BLAS and LAPACK for Intel® 64
          Intel® Xeon Phi™ coprocessor support
          Cluster support for Intel® 64
          Intel MKL core libraries for IA-32
          Fortran 95 interfaces for BLAS and LAPACK for IA-32
          Cluster support for IA-32
       Intel Integrated Performance Primitives 8.2 Update 1
          Intel IPP single-threaded libraries for Intel® 64
             General package
          Intel IPP single-threaded libraries for IA-32
             General package
       Intel Threading Building Blocks 4.3 Update 1
       Intel VTune Amplifier XE 2015 Update 1
          Command-line interface
          Graphical user interface
          Event-based sampling driver
       Intel Inspector XE 2015 Update 1
          Command-line interface
          Graphical user interface
       Intel Advisor XE 2015 Update 1
          Command-line interface
          Graphical user interface

Instalasi Intel(R) Parallel Studio XE di Ubuntu

Untuk menjalankan TIM-OS kita memerlukan Intel(R) Parallel Studio, disini kita menggunakan versi  2015 Update 1 untuk Linux.

Ketika pertama kali mencoba melakukan instalasi, pada tahap 1, yaitu memerika prasyarat sistem, installer memberi umpan balik seperti berikut :

There are one or more optional unresolved issues. It is highly recommended to
resolve them all before you continue the installation. You can fix them without
exiting from the installation and re-check. Or you can quit from the
installation, fix them and run the installation again.
--------------------------------------------------------------------------------
Missing optional prerequisites
-- Intel(R) MPI Library, Development Kit 5.0 Update 2 for Linux* OS: Unsupported
OS
-- Intel(R) Trace Analyzer and Collector 9.0 Update 2 for Linux* OS: Unsupported
OS
-- Intel(R) VTune(TM) Amplifier XE 2015 Update 1: Unsupported OS
-- Intel(R) Inspector XE 2015 Update 1: Unsupported OS
-- Intel(R) Advisor XE 2015 Update 1: Unsupported OS
-- Intel(R) Parallel Studio XE 2015 Update 1 Composer Edition for C++ Linux*:
Unsupported OS
-- Intel(R) Parallel Studio XE 2015 Update 1 Composer Edition for Fortran
Linux*: Unsupported OS
-- Intel(R) Parallel Studio XE 2015 Update 1 Composer Edition for Linux*:
Unsupported OS
--------------------------------------------------------------------------------
1. Skip missing optional prerequisites [default]
2. Show the detailed info about issue(s)
3. Re-check the prerequisites
h. Help
b. Back to the previous menu
q. Quit
--------------------------------------------------------------------------------
Please type a selection or press "Enter" to accept default choice [1]:

Sepertinya OS yang digunakan tidak didukung oleh  Instalasi Intel(R) Parallel Studio XE 2015 update 1, berikut adalah pesannya :

Step 1 of 7 | Prerequisites > Missing Optional Prerequisite
--------------------------------------------------------------------------------
Detected operating system is not supported. Supported operating systems for this
release are:
    - Ubuntu* 12.04 (Intel(R) 64), 14.04 (Intel(R) 64);
    - SUSE Linux Enterprise Server* 11 (Intel(R) 64), 12 (Intel(R) 64);
    - Red Hat Enterprise Linux* 6 (Intel(R) 64), 7 (Intel(R) 64);
    - Fedora* 20 (Intel(R) 64), 21 (Intel(R) 64);
    - Debian* 6.0 (Intel(R) 64), 7.0 (Intel(R) 64);
    - CentOS* 6 (Intel(R) 64);

Karena mesin yang digunakan untuk instalasi ini adalah mesin 32 bit :

(parallel_studio_xe_2015_update1) file /sbin/init
/sbin/init: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.24, BuildID[sha1]=0x38b96d0043362753120e731e31c8f65c5e67e87f, stripped

Sebelum lanjut, kita harus memenuhi prasyarat yang diminta oleh installer.