CudaMiner Installation In Ubuntu 12.04 LTS Using CUDA Toolkit 5.5 And "Additional NVIDIA Drivers"

Author's Note 1: It is my standard policy to put too much info into guides so that those who are searching for specific problems they come across will find the offending text in their searches. With luck, your "build error" search sent you here.

Author's Note 2: It's not as bad as it looks (I've included lots of output and error messages for easy searching)!

Author's Note 3: I won't be much help for you in diagnosing your errors, but am happy to tweak the text below if something is unclear.

Conventions: I include both the commands you type in your Terminal and some of the output from these commands, the output being where most of the errors appear that I work on in the discussion.

Input is formatted as below:

Text you put in (copy + paste should be fine)

Output is formatted as below:

Text you get out (for checking results and reproducing errors)

1. Introduction

This work began as an attempt to build a CUDA-friendly version of the molecular dynamics package GROMACS (which will come later) but, for reasons stemming from a new local Syracuse Meetup Group (Bitcoin's of New York – Miner's of Syracuse. Consider joining!), the formation of our very own local mining pool (Salt City Miners, miner.saltcityminers.com. Consider joining!), plus a "what the hell" to see if it was an easy build or not, transformed into the CudaMiner-centric compiling post you see here.

NOTE: This will be a 64-bit-centric install but I'll include 32-bit content as I've found the info on other sites.

2. Installing The NVIDIA Drivers (Two Methods, The Easy One Described)

Having run through this process many times in a fresh install of Ubuntu 12.04 LTS (so nothing else is on the machine except 12.04 LTS, its updates, a few extra installs, and the CUDA/CudaMiner codes), I can say that what is below should work without hitch AFTER you install the NVIDIA drivers. Once your NVIDIA card is installed and Ubuntu recognizes it, you've two options.

2A. Install The Drivers From An NVIDIA Download (The Hard Version)

A few websites (and several repostings of the same content) describe the process of installing the NVIDIA drivers the olde-fashioned way, in which you'll see references to "blacklist nouveau," "sudo service lightdm stop," Ctrl+Alt+F1 (to get you to a text-only session), etc. You hopefully don't need to do this much work for your own NVIDIA install, as Ubuntu will do it for you (with only one restart required).

2B. Install The Drivers After The "Restricted Drivers Available" Pop-Up Or Go To System Settings > Available Drivers (The Easy, Teenage New York Version)

I took the easy way out by letting Ubuntu do the dirty work. The result is the installation of the (currently, as of 28 Dec 2013) v. 319 NVIDIA accelerated graphics driver. For my NVIDIA cards (GTX 690 and a GTX 650 Ti, although I assume it's similar for a whole class of NVIDIA cards), you're (currently, check the date again) given the option of v. 304. Don't! I've seen several mentions of CudaMiner (and some of the cuds toolkit) requiring v. 319.

2013dec28_nvidia_1

Caption: You may see it in the upper right (after an install or if you've not clicked on it before)

2013dec28_nvidia_2

Caption: Or System Settings > Additional Drivers

2013dec28_nvidia_3

Caption: Either way, you'll hopefully get to an NVIDIA driver list like above.

3. Pre-CUDA Toolkit Install

There are a few apt-get's you need to do before installing the CUDA Toolkit (or, at least, the consensus is that these must be done. I've not seen a different list in any posts and I didn't bother to install one-by-one to see which of these might not be needed).

If you perform the most commonly posted apt-get (plus and update and upgrade if you've not done so lately):

user@host:~/$ sudo apt-get update
user@host:~/$ sudo apt-get upgrade
user@host:~/$ sudo apt-get install freeglut3-dev build-essential libx11-dev libxmu-dev libxi-dev libgl1-mesa-glx libglu1-mesa libglu1-mesa-dev

You'll get the following error from a fresh 12.04 LTS install:

Reading package lists… Done
Building dependency tree
Reading state information… Done
libglu1-mesa is already the newest version.
libglu1-mesa set to manually installed.
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
libgl1-mesa-glx : Depends: libglapi-mesa (= 8.0.4-0ubuntu0.6)
Recommends: libgl1-mesa-dri (>= 7.2)
E: Unable to correct problems, you have held broken packages.

The solution here is simple. Add libglapi-mesa and libgl1-mesa-dri to your install.

user@host:~/$ sudo apt-get install freeglut3-dev build-essential libx11-dev libxmu-dev libxi-dev libgl1-mesa-glx libglu1-mesa libglu1-mesa-dev libglapi-mesa libgl1-mesa-dri

Doing this will add a bunch of programs and libraries (listed below):

The following extra packages will be installed:
dpkg-dev freeglut3 g++ g++-4.6 libalgorithm-diff-perl libalgorithm-diff-xs-perl
libalgorithm-merge-perl libdpkg-perl libdrm-dev libgl1-mesa-dev libice-dev libkms1 libllvm3.0
libpthread-stubs0 libpthread-stubs0-dev libsm-dev libstdc++6-4.6-dev libtimedate-perl libx11-doc
libxau-dev libxcb1-dev libxdmcp-dev libxext-dev libxmu-headers libxt-dev mesa-common-dev
x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev xorg-sgml-doctools
xserver-xorg xserver-xorg-core xserver-xorg-input-evdev xtrans-dev
Suggested packages:
debian-keyring g++-multilib g++-4.6-multilib gcc-4.6-doc libstdc++6-4.6-dbg libglide3
libstdc++6-4.6-doc libxcb-doc xfonts-100dpi xfonts-75dpi
The following packages will be REMOVED:
libgl1-mesa-dri-lts-raring libgl1-mesa-glx-lts-raring libglapi-mesa-lts-raring
libxatracker1-lts-raring x11-xserver-utils-lts-raring xserver-common-lts-raring
xserver-xorg-core-lts-raring xserver-xorg-input-all-lts-raring xserver-xorg-input-evdev-lts-raring
xserver-xorg-input-mouse-lts-raring xserver-xorg-input-synaptics-lts-raring
xserver-xorg-input-vmmouse-lts-raring xserver-xorg-input-wacom-lts-raring xserver-xorg-lts-raring
xserver-xorg-video-all-lts-raring xserver-xorg-video-ati-lts-raring
xserver-xorg-video-cirrus-lts-raring xserver-xorg-video-fbdev-lts-raring
xserver-xorg-video-intel-lts-raring xserver-xorg-video-mach64-lts-raring
xserver-xorg-video-mga-lts-raring xserver-xorg-video-modesetting-lts-raring
xserver-xorg-video-neomagic-lts-raring xserver-xorg-video-nouveau-lts-raring
xserver-xorg-video-openchrome-lts-raring xserver-xorg-video-r128-lts-raring
xserver-xorg-video-radeon-lts-raring xserver-xorg-video-s3-lts-raring
xserver-xorg-video-savage-lts-raring xserver-xorg-video-siliconmotion-lts-raring
xserver-xorg-video-sis-lts-raring xserver-xorg-video-sisusb-lts-raring
xserver-xorg-video-tdfx-lts-raring xserver-xorg-video-trident-lts-raring
xserver-xorg-video-vesa-lts-raring xserver-xorg-video-vmware-lts-raring
The following NEW packages will be installed:
build-essential dpkg-dev freeglut3 freeglut3-dev g++ g++-4.6 libalgorithm-diff-perl
libalgorithm-diff-xs-perl libalgorithm-merge-perl libdpkg-perl libdrm-dev libgl1-mesa-dev
libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglu1-mesa-dev libice-dev libkms1 libllvm3.0
libpthread-stubs0 libpthread-stubs0-dev libsm-dev libstdc++6-4.6-dev libtimedate-perl libx11-dev
libx11-doc libxau-dev libxcb1-dev libxdmcp-dev libxext-dev libxi-dev libxmu-dev libxmu-headers
libxt-dev mesa-common-dev x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev
xorg-sgml-doctools xserver-xorg xserver-xorg-core xserver-xorg-input-evdev xtrans-dev

And, remarkably, that's it for the pre-install.

4. CUDA Toolkit 5.5(.22) Install

The CUDA Toolkit install starts with its 810 MB download at developer.NVIDIA.com/cuda-downloads.

Obviously, be aware of the 32- and 64-bit options. Also, the .deb doesn't currently download, leaving you to grab the .run file (same difference, I haven't bothered to find out why the .deb doesn't fly yet).

Off to your Terminal and into the Downloads folder:

user@host:~/$ cd Downloads
user@host:~/Downloads$ chmod +x cuda_5.5.22_linux_64.run
user@host:~/Downloads$ sudo ./cuda_5.5.22_linux_64.run

Which will produce:

Logging to /tmp/cuda_install_14755.log
Using more to view the EULA.
End User License Agreement
————————–
. . .
and cannot be linked to any personally identifiable
information. Personally identifiable information such as your
username or hostname is not collected.

————————————————————-

Finally, some input to be had after the scrolling:

Do you accept the previously read EULA? (accept/decline/quit): accept     
Install NVIDIA Accelerated Graphics Driver for Linux-x86_64 319.37? ((y)es/(n)o/(q)uit): n
Install the CUDA 5.5 Toolkit? ((y)es/(n)o/(q)uit): y
Enter Toolkit Location [ default is /usr/local/cuda-5.5 ]: 
Install the CUDA 5.5 Samples? ((y)es/(n)o/(q)uit): y
Enter CUDA Samples Location [ default is /home/user/NVIDIA_CUDA-5.5_Samples ]: 

NOTE 1: Don't install the NVIDIA Accelerated Graphics Driver!
NOTE 2: Yes, install the Toolkit.
NOTE 3: I will assume this location for all of the below, setting the location in the PATH.
NOTE 4: I installed the samples for testing (and found a few extra things that need installation for them).
NOTE 5: Default is fine. Once built and tested, can be deleted (although the Mandelbrot is a keeper)

Installing the CUDA Toolkit in /usr/local/cuda-5.5 …
Installing the CUDA Samples in /home/user/NVIDIA_CUDA-5.5_Samples …
Copying samples to /home/user/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples now…
Finished copying samples.

===========
= Summary =
===========

Driver: Not Selected
Toolkit: Installed in /usr/local/cuda-5.5
Samples: Installed in /home/user/NVIDIA_CUDA-5.5_Samples

* Please make sure your PATH includes /usr/local/cuda-5.5/bin

* Please make sure your LD_LIBRARY_PATH
* for 32-bit Linux distributions includes /usr/local/cuda-5.5/lib
* for 64-bit Linux distributions includes /usr/local/cuda-5.5/lib64:/lib
* OR
* for 32-bit Linux distributions add /usr/local/cuda-5.5/lib
* for 64-bit Linux distributions add /usr/local/cuda-5.5/lib64 and /lib
* to /etc/ld.so.conf and run ldconfig as root

* To uninstall CUDA, remove the CUDA files in /usr/local/cuda-5.5
* Installation Complete

Please see CUDA_Getting_Started_Linux.pdf in /usr/local/cuda-5.5/doc/pdf for detailed information on setting up CUDA.

***WARNING: Incomplete installation! This installation did not install the CUDA Driver. A driver of version at least 319.00 is required for CUDA 5.5 functionality to work.
To install the driver using this installer, run the following command, replacing with the name of this run file:
sudo
.run -silent -driver

Logfile is /tmp/cuda_install_14755.log

And ignore the WARNING.

As per the "make sure" above, add the CUDA distro folders to your path and LD_LIBRARY_PATH (I chose not to modify ld.so.conf)

user@host:~/Downloads$ cd
user@host:~/$ nano .bashrc

Add the PATH and LD_LIBRARY_PATH as follows:

PATH=$PATH:/usr/local/cuda-5.5/bin
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-5.5/lib64:/lib

And then source the .bashrc file.

user@host:~/$ source .bashrc

5. NVIDIA_CUDA-5.5_Samples (And Finishing The Toolkit Install To Build CudaMiner)

The next set of installs and file modifications came from attempting to build the Samples in the NVIDIA_CUDA-5.5_Samples (or NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples depending on how your install did it) library, during which time I think I managed to hit all of the post-Toolkit install modifications needed to make the CudaMiner build problem-free. The OpenMPI install is optional, but I do hate error messages.

5A. Error 1: /usr/bin/ld: cannot find -lcuda

My first make attempt produced the following error:

user@host:~/$ cd NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples
user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples$ make

make[1]: Entering directory `/home/user/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/0_Simple/asyncAPI'
"/usr/local/cuda-5.5"/bin/nvcc -ccbin g++ -Ihttp://www.somewhereville.com/common/inc -m64 -gencode arch=compute_10,code=sm_10 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=\"sm_35,compute_35\" -o asyncAPI.o -c asyncAPI.cu
. . .
"/usr/local/cuda-5.5"/bin/nvcc -ccbin g++ -Ihttp://www.somewhereville.com/common/inc -m64 -o vectorAddDrv.o -c vectorAddDrv.cpp
"/usr/local/cuda-5.5"/bin/nvcc -ccbin g++ -m64 -o vectorAddDrv vectorAddDrv.o -L/usr/lib/NVIDIA-current -lcuda
/usr/bin/ld: cannot find -lcuda
collect2: ld returned 1 exit status
make[1]: *** [vectorAddDrv] Error 1
make[1]: Leaving directory `/home/user/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/0_Simple/vectorAddDrv'
make: *** [0_Simple/vectorAddDrv/Makefile.ph_build] Error 2

This is solved by making a symbolic link for libcuda.so out of /usr/lib/NVIDIA-319/ and into /usr/lib/

NOTE: It doesn't matter what directory you do this from. I've left off the NVIDIA_CUDA-5.5_Samples/ yadda yadda below.

user@host:~/$ sudo ln -s /usr/lib/NVIDIA-319/libcuda.so /usr/lib/libcuda.so

If you're working through the build process and hit the error, run a "make clean" before rerunning.

5B. WARNING – No MPI compiler found.

The second build attempt produced the MPI Warning above.

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples$ make

make[1]: Entering directory `/home/user/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/0_Simple/asyncAPI'
"/usr/local/cuda-5.5"/bin/nvcc -ccbin g++ -Ihttp://www.somewhereville.com/common/inc -m64 -gencode arch=compute_10,code=sm_10 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=\"sm_35,compute_35\" -o asyncAPI.o -c asyncAPI.cu
"/usr/local/cuda-5.5"/bin/nvcc -ccbin g++ -m64 -o asyncAPI asyncAPI.o
. . .
cp simpleCubemapTexture http://www.somewhereville.com/bin/x86_64/linux/release
make[1]: Leaving directory `/home/user/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/0_Simple/simpleCubemapTexture'
———————————————————————————————–
WARNING – No MPI compiler found.
———————————————————————————————–
CUDA Sample "simpleMPI" cannot be built without an MPI Compiler.
This will be a dry-run of the Makefile.
For more information on how to set up your environment to build and run this
sample, please refer the CUDA Samples documentation and release notes
———————————————————————————————–
make[1]: Entering directory `/home/user/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/0_Simple/simpleMPI'
[@] mpicxx -Ihttp://www.somewhereville.com/common/inc -o simpleMPI.o -c simpleMPI.cpp
. . .
mkdir -p http://www.somewhereville.com/bin/x86_64/linux/release
cp histEqualizationNPP http://www.somewhereville.com/bin/x86_64/linux/release
make[1]: Leaving directory `/home/user/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/7_CUDALibraries/histEqualizationNPP'
Finished building CUDA samples

But otherwise finishes successfully.

To get around this warning, install OpenMPI (which is needed for multi-board GROMACS runs anyway. But, again, not needed for CudaMiner). The specific issue is the need for mpicc, which is in libopenmpi-dev (not openmpi-bin or openmpi-common).

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples$ mpicc
The program 'mpicc' can be found in the following packages:
* lam4-dev
* libmpich-mpd1.0-dev
* libmpich-shmem1.0-dev
* libmpich1.0-dev
* libmpich2-dev
* libopenmpi-dev
* libopenmpi1.5-dev
Try: sudo apt-get install

For completeness, I grab all three (and I'm ingnoring the NVIDIA_CUDA-5.5_Samples directory structure below).

user@host:~/$ sudo apt-get install openmpi-bin openmpi-common libopenmpi-dev

Running mpicc will now produce the following (so it's there):

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples$ mpicc
gcc: fatal error: no input files
compilation terminated.

Now run a "make clean" if needed and make. The build should go without problem.

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples$ make

make[1]: Entering directory `/home/user/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/0_Simple/asyncAPI'
"/usr/local/cuda-5.5"/bin/nvcc -ccbin g++ -Ihttp://www.somewhereville.com/common/inc -m64 -gencode arch=compute_10,code=sm_10 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=\"sm_35,compute_35\" -o asyncAPI.o -c asyncAPI.cu
"/usr/local/cuda-5.5"/bin/nvcc -ccbin g++ -m64 -o asyncAPI asyncAPI.o
mkdir -p http://www.somewhereville.com/bin/x86_64/linux/release
. . .
mkdir -p http://www.somewhereville.com/bin/x86_64/linux/release
cp histEqualizationNPP http://www.somewhereville.com/bin/x86_64/linux/release
make[1]: Leaving directory `/home/user/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/7_CUDALibraries/histEqualizationNPP'
Finished building CUDA samples

5C. Needed post-processing (lib glut, cuda.conf, NVIDIA.conf, and ldconfig)

The next round of problems stemmed from not being able to run the randomFog program in the new ~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/bin/x86_64/linux/release folder. I suspect the steps taken to remedy this also make all future CUDA-specific work easier, so list the issues and clean-up steps below.

Out of the list of build samples, I selected a few that worked without issue and, finally, randomFog that decidedly had issues:

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/$ cd bin/x86_64/linux/release
user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/bin/x86_64/linux/release$ ls
alignedTypes HSOpticalFlow simpleCUBLAS
asyncAPI imageDenoising simpleCUDA2GL
bandwidthTest imageSegmentationNPP simpleCUFFT
batchCUBLAS inlinePTX simpleDevLibCUBLAS
bicubicTexture interval simpleGL
bilateralFilter jpegNPP simpleHyperQ
bindlessTexture lineOfSight simpleIPC
binomialOptions Mandelbrot simpleLayeredTexture
BlackScholes marchingCubes simpleMPI
boxFilter matrixMul simpleMultiCopy
boxFilterNPP matrixMulCUBLAS simpleMultiGPU
cdpAdvancedQuicksort matrixMulDrv simpleP2P
cdpBezierTessellation matrixMulDynlinkJIT simplePitchLinearTexture
cdpLUDecomposition matrixMul_kernel64.ptx simplePrintf
cdpQuadtree MC_EstimatePiInlineP simpleSeparateCompilation
cdpSimplePrint MC_EstimatePiInlineQ simpleStreams
cdpSimpleQuicksort MC_EstimatePiP simpleSurfaceWrite
clock MC_EstimatePiQ simpleTemplates
concurrentKernels MC_SingleAsianOptionP simpleTexture
conjugateGradient mergeSort simpleTexture3D
conjugateGradientPrecond MersenneTwisterGP11213 simpleTextureDrv
convolutionFFT2D MonteCarloMultiGPU simpleTexture_kernel64.ptx
convolutionSeparable nbody simpleVoteIntrinsics
convolutionTexture newdelete simpleZeroCopy
cppIntegration oceanFFT smokeParticles
cppOverload particles SobelFilter
cudaOpenMP postProcessGL SobolQRNG
dct8x8 ptxjit sortingNetworks
deviceQuery quasirandomGenerator stereoDisparity
deviceQueryDrv radixSortThrust template
dwtHaar1D randomFog template_runtime
dxtc recursiveGaussian threadFenceReduction
eigenvalues reduction threadMigration
fastWalshTransform scalarProd threadMigration_kernel64.ptx
FDTD3d scan transpose
fluidsGL segmentationTreeThrust vectorAdd
freeImageInteropNPP shfl_scan vectorAddDrv
FunctionPointers simpleAssert vectorAdd_kernel64.ptx
grabcutNPP simpleAtomicIntrinsics volumeFiltering
histEqualizationNPP simpleCallback volumeRender
histogram simpleCubemapTexture

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/bin/x86_64/linux/release$ ./randomFog

And you get the following error:

./randomFog: error while loading shared libraries: libcurand.so.5.5: cannot open shared object file: No such file or directory

I originally thought this error might have something to with libglut based on other install sites I ran across. I therefore took the step of adding the symbolic link from /usr/lib/x86_64-linux-gnu to /usr/lib

user@host:~$ sudo ln -s /usr/lib/x86_64-linux-gnu/libglut.so.3 /usr/lib/libglut.so

That said, same issue:

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/bin/x86_64/linux/release$ ./randomFog
./randomFog: error while loading shared libraries: libcurand.so.5.5: cannot open shared object file: No such file or directory

I then found references to adding a cuda.conf file to /etc/ld.so.conf.d – and so did that (doesn't help but it came up enough that I suspect it doesn't hurt either).

user@host:~$ sudo nano /etc/ld.so.conf.d/cuda.conf 

This file should contain the following:

/usr/local/cuda-5.5/lib64
/usr/local/cuda-5.5/lib

Which also didn't help.

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/bin/x86_64/linux/release$ ./randomFog 

./randomFog: error while loading shared libraries: libcurand.so.5.5: cannot open shared object file: No such file or directory

To find the location (or presence) of libcurand, ldconfig -v

user@host:~/$ ldconfig -v

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/bin/x86_64/linux/release$ ldconfig -v
/sbin/ldconfig.real: Path `/lib/x86_64-linux-gnu' given more than once
/sbin/ldconfig.real: Path `/usr/lib/x86_64-linux-gnu' given more than once
/usr/local/cuda-5.5/lib64:
libcuinj64.so.5.5 -> libcuinj64.so.5.5.22
libcufft.so.5.5 -> libcufft.so.5.5.22
libcurand.so.5.5 -> libcurand.so.5.5.22
libcusparse.so.5.5 -> libcusparse.so.5.5.22
. . .
libnvToolsExt.so.1 -> libnvToolsExt.so.1.0.0
/usr/local/cuda-5.5/lib:
libcufft.so.5.5 -> libcufft.so.5.5.22
libcurand.so.5.5 -> libcurand.so.5.5.22
libcusparse.so.5.5 -> libcusparse.so.5.5.22
. . .
/usr/lib/NVIDIA-319/tls: (hwcap: 0x8000000000000000)
libNVIDIA-tls.so.319.32 -> libNVIDIA-tls.so.319.32
/usr/lib32/NVIDIA-319/tls: (hwcap: 0x8000000000000000)
libNVIDIA-tls.so.319.32 -> libNVIDIA-tls.so.319.32
/sbin/ldconfig.real: Can't create temporary cache file /etc/ld.so.cache~: Permission denied

Present twice. Instead of risking making multiple symbolic links as I walked through the dependency gauntlet, I stumbled across another reference in the form of a new /etc/ld.so.conf.d/NVIDIA.conf that contains the same content as cuda.conf (so one may not be needed, but I didn't bother to backtrack to see. Happy to change the page if someone says otherwise).

user@host:~/$ sudo nano /etc/ld.so.conf.d/NVIDIA.conf

/usr/local/cuda-5.5/lib64
/usr/local/cuda-5.5/lib

Then run ldconfig.

user@host:~/$ sudo ldconfig

With that, randomFog works just fine (and you can assume that a problem in one is a problem in several. Having not taken the full symbolic link route in favor of adding to /etc/ld.so.conf.d, I'm assuming I hit most of the potential errors for the other programs.

user@host:~/NVIDIA_CUDA-5.5_Samples/NVIDIA_CUDA-5.5_Samples/bin/x86_64/linux/release$ ./randomFog 

Random Fog
==========

CURAND initialized

Random number visualization

6. Build CudaMiner

The good news is that there are only a few more steps. The bad news is that any errors you come across in your attempt to build CudaMiner that relate to NOT having done the above are (likely) not represented here, so hopefully your search was sufficiently vague.

Download CudaMiner-master.zip from Christian Buchner's github account. Extracting CudaMiner-master.zip (with unzip, not gunzip. Damn Windows users) and running configure produces only one obvious error.

user@host:~/WHEREVER_YOU_ARE/$ cd
user@host:~/$ cd Downloads
user@host:~/Downloads$ unzip CudaMiner-master.zip 
user@host:~/Downloads$ cd CudaMiner-master/
user@host:~/Downloads/CudaMiner-master$ chmod a+wrx configure
user@host:~/Downloads/CudaMiner-master$ ./configure

checking build system type… x86_64-unknown-linux-gnu
checking host system type… x86_64-unknown-linux-gnu
checking target system type… x86_64-unknown-linux-gnu
checking for a BSD-compatible install… /usr/bin/install -c
. . .
checking for gawk… (cached) mawk
checking for curl-config… no
checking whether libcurl is usable… no
configure: error: Missing required libcurl >= 7.15.2

This error is remedied by installing libcurl4-gnutls-dev.

user@host:~/Downloads/CudaMiner-master$ sudo apt-get install libcurl4-gnutls-dev 

Which adds and modifies the following from my clean 12.04 LTS install and update

The following packages were automatically installed and are no longer required:
gir1.2-ubuntuoneui-3.0 libxcb-dri2-0 libxrandr-ltsr2 libubuntuoneui-3.0-1 libxvmc1 thunderbird-globalmenu
libllvm3.2
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
comerr-dev krb5-multidev libgcrypt11-dev libgnutls-dev libgnutls-openssl27 libgnutlsxx27 libgpg-error-dev
libgssrpc4 libidn11-dev libkadm5clnt-mit8 libkadm5srv-mit8 libkdb5-6 libkrb5-dev libldap2-dev
libp11-kit-dev librtmp-dev libtasn1-3-dev zlib1g-dev
Suggested packages:
krb5-doc libcurl3-dbg libgcrypt11-doc gnutls-doc gnutls-bin krb5-user
The following NEW packages will be installed:
comerr-dev krb5-multidev libcurl4-gnutls-dev libgcrypt11-dev libgnutls-dev libgnutls-openssl27
libgnutlsxx27 libgpg-error-dev libgssrpc4 libidn11-dev libkadm5clnt-mit8 libkadm5srv-mit8 libkdb5-6
libkrb5-dev libldap2-dev libp11-kit-dev librtmp-dev libtasn1-3-dev zlib1g-dev

After a make clean, configure and make for CudaMiner went without problem.

user@host:~/Downloads/CudaMiner-master$ make clean
user@host:~/Downloads/CudaMiner-master$ ./configure

checking build system type… x86_64-unknown-linux-gnu
checking host system type… x86_64-unknown-linux-gnu
checking target system type… x86_64-unknown-linux-gnu
checking for a BSD-compatible install… /usr/bin/install -c
checking whether build environment is sane… yes
checking for a thread-safe mkdir -p… /bin/mkdir -p
. . .
configure: creating ./config.status
config.status: creating Makefile
config.status: creating compat/Makefile
config.status: creating compat/jansson/Makefile
config.status: creating cpuminer-config.h
config.status: cpuminer-config.h is unchanged
config.status: executing depfiles commands

user@host:~/Downloads/CudaMiner-master$ make

make all-recursive
make[1]: Entering directory `/home/user/Downloads/CudaMiner-master'
Making all in compat
make[2]: Entering directory `/home/user/Downloads/CudaMiner-master/compat'
Making all in jansson
make[3]: Entering directory `/home/user/Downloads/CudaMiner-master/compat/jansson'
. . .
./spinlock_kernel.cu(387): Warning: Cannot tell what pointer points to, assuming global memory space
./spinlock_kernel.cu(387): Warning: Cannot tell what pointer points to, assuming global memory space
./spinlock_kernel.cu(387): Warning: Cannot tell what pointer points to, assuming global memory space
. . .
nvcc -g -O2 -Xptxas "-abi=no -v" -arch=compute_10 –maxrregcount=64 –ptxas-options=-v -I./compat/jansson -o legacy_kernel.o -c legacy_kernel.cu
./legacy_kernel.cu(310): Warning: Cannot tell what pointer points to, assuming global memory space
./legacy_kernel.cu(310): Warning: Cannot tell what pointer points to, assuming global memory space
./legacy_kernel.cu(310): Warning: Cannot tell what pointer points to, assuming global memory space
. . .
g++ -g -O2 -pthread -L/usr/local/cuda/lib64 -o cudaminer cudaminer-cpu-miner.o cudaminer-util.o cudaminer-sha2.o cudaminer-scrypt.o salsa_kernel.o spinlock_kernel.o legacy_kernel.o fermi_kernel.o kepler_kernel.o test_kernel.o titan_kernel.o -L/usr/lib/x86_64-linux-gnu -lcurl -Wl,-Bsymbolic-functions -Wl,-z,relro compat/jansson/libjansson.a -lpthread -lcudart -fopenmp
make[2]: Leaving directory `/home/user/Downloads/CudaMiner-master'
make[1]: Leaving directory `/home/user/Downloads/CudaMiner-master'

A few warnings (well, several hundred of the same warnings) appeared during the build process (but don't affect the program operation. Just pointing them out above).

With luck, you should be able to run a benchmark calculation immediately.

user@host:~/Downloads/CudaMiner-master$ ./cudaminer -d 0 -i 0 --benchmark

*** CudaMiner for NVIDIA GPUs by Christian Buchner ***
This is version 2013-12-18 (beta)
based on pooler-cpuminer 2.3.2 (c) 2010 Jeff Garzik, 2012 pooler
Cuda additions Copyright 2013 Christian Buchner
My donation address: LKS1WDKGED647msBQfLBHV3Ls8sveGncnm

[2013-12-25 00:05:38] 1 miner threads started, using 'scrypt' algorithm.
[2013-12-25 00:05:58] GPU #0: GeForce GTX 690 with compute capability 3.0
[2013-12-25 00:05:58] GPU #0: the 'K' kernel requires single memory allocation
[2013-12-25 00:05:58] GPU #0: interactive: 0, tex-cache: 0 , single-alloc: 1
[2013-12-25 00:05:58] GPU #0: Performing auto-tuning (Patience…)
[2013-12-25 00:05:58] GPU #0: maximum warps: 447
[2013-12-25 00:07:40] GPU #0: 288.38 khash/s with configuration K27x4
[2013-12-25 00:07:40] GPU #0: using launch configuration K27x4
[2013-12-25 00:07:40] GPU #0: GeForce GTX 690, 6912 hashes, 0.06 khash/s
[2013-12-25 00:07:40] Total: 0.06 khash/s
[2013-12-25 00:07:40] GPU #0: GeForce GTX 690, 3456 hashes, 141.56 khash/s
[2013-12-25 00:07:40] Total: 141.56 khash/s
[2013-12-25 00:07:43] GPU #0: GeForce GTX 690, 708480 hashes, 251.11 khash/s
[2013-12-25 00:07:43] Total: 251.11 khash/s
[2013-12-25 00:07:48] GPU #0: GeForce GTX 690, 1257984 hashes, 251.19 khash/s
[2013-12-25 00:07:48] Total: 251.19 khash/s
. . .

Then spend the rest of the week optimizing parameters for your particular card and mining proclivity:

user@host:~/Downloads/CudaMiner-master$ ./cudaminer -h
	   *** CudaMiner for NVIDIA GPUs by Christian Buchner ***
	             This is version 2013-12-18 (beta)
	based on pooler-cpuminer 2.3.2 (c) 2010 Jeff Garzik, 2012 pooler
	       Cuda additions Copyright 2013 Christian Buchner
	   My donation address: LKS1WDKGED647msBQfLBHV3Ls8sveGncnm

Usage: cudaminer [OPTIONS]
Options:
  -a, --algo=ALGO       specify the algorithm to use
                          scrypt    scrypt(1024, 1, 1) (default)
                          sha256d   SHA-256d
  -o, --url=URL         URL of mining server (default: http://127.0.0.1:9332/)
  -O, --userpass=U:P    username:password pair for mining server
  -u, --user=USERNAME   username for mining server
  -p, --pass=PASSWORD   password for mining server
      --cert=FILE       certificate for mining server using SSL
  -x, --proxy=[PROTOCOL://]HOST[:PORT]  connect through a proxy
  -t, --threads=N       number of miner threads (default: number of processors)
  -r, --retries=N       number of times to retry if a network call fails
                          (default: retry indefinitely)
  -R, --retry-pause=N   time to pause between retries, in seconds (default: 30)
  -T, --timeout=N       network timeout, in seconds (default: 270)
  -s, --scantime=N      upper bound on time spent scanning current work when
                          long polling is unavailable, in seconds (default: 5)
      --no-longpoll     disable X-Long-Polling support
      --no-stratum      disable X-Stratum support
  -q, --quiet           disable per-thread hashmeter output
  -D, --debug           enable debug output
  -P, --protocol-dump   verbose dump of protocol-level activities
      --no-autotune     disable auto-tuning of kernel launch parameters
  -d, --devices         takes a comma separated list of CUDA devices to use.
                        This implies the -t option with the threads set to the
                        number of devices.
  -l, --launch-config   gives the launch configuration for each kernel
                        in a comma separated list, one per device.
  -i, --interactive     comma separated list of flags (0/1) specifying
                        which of the CUDA device you need to run at inter-
                        active frame rates (because it drives a display).
  -C, --texture-cache   comma separated list of flags (0/1) specifying
                        which of the CUDA devices shall use the texture
                        cache for mining. Kepler devices will profit.
  -m, --single-memory   comma separated list of flags (0/1) specifying
                        which of the CUDA devices shall allocate their
                        scrypt scratchbuffers in a single memory block.
  -H, --hash-parallel   1 to enable parallel SHA256 hashing on the CPU. May
                        use more CPU overall, but distributes hashing load
                        neatly across all CPU cores. 0 is now the default
                        which assigns one static CPU core to each GPU.
  -S, --syslog          use system log for output messages
  -B, --background      run the miner in the background
      --benchmark       run in offline benchmark mode
  -c, --config=FILE     load a JSON-format configuration file
  -V, --version         display version information and exit
  -h, --help            display this help text and exit

I've only had a few problems with CudaMiner to date. The most annoying problem has been the inability to run tests to optimize card performance without having to put the machine to sleep and wake it back up again (better than a full restart). CudaMiner will, without this, simply hang on a script line:

[2013-12-25 00:49:08] 1 miner threads started, using 'scrypt' algorithm.

The sleep + wake does the trick, although I'd love to find out how to not have this happen.

The second annoying problem was:

". . . result does not validate on CPU (i=NNNN, s=0)!

This error is due to your "K16x16" configuration (the most prominent one I've found in google searches, so placed here to help others find it. Your values may vary) being too much for the card (so vary them down a spell until you don't get there error). There's a wealth of proper card settings available on the litecoin hardware comparison site, so I direct you there:

litecoin.info/Mining_hardware_comparison

7. And Finally. . .

By all accounts, CudaMiner is a much faster mining tool for NVIDIA owners. To that end, please note that Christian Buchner has made your life much easier (and your virtual wallet hopefully a little fuller). As mentioned above, his donation address is:

LKS1WDKGED647msBQfLBHV3Ls8sveGncnm

Do consider showing him some love.

This post was made in the interest of helping others get their mining going. If this guide helped and you score blocks early, my wallet's always open as well (can't blame someone for trying).

Litecoin: LTmicpwpGgrZiyiJmMUdyqq4CG8CqiBqrm
Dogecoin: DBwXMoQ4scAqZfYUJgc3SYqTED7eywSHdB

The timing for getting the guide up is based on a new mining operation here in Syracuse, NY in the form of Salt City Miners, currently the Cloud City of mining operations (also appropriate for the weather conditions). Parties interested in adding their power to the fold are more than welcome to sign up at miner.saltcityminers.com/.

2013dec28_scm_logo

And don't forget the Meetup group: Syracuse Meetup Group – Bitcoin's of New York – Miner's of Syracuse

Compiling LAMMPS (3Apr13, But Likely Others) In Ubuntu 10.04 Part 1. Using MPICH2 And FFTW2 (And Ubuntu Notes On Installing Intel Fortran And C++ Composers XE for Linux)

I'll qualify this post by saying that (1) I have given up on Ubuntu 11.x and 12.x because they are consistently unstable on my hardware (so, if you have issues running this installation on those versions, I may not be of much help (although I suspect things should work)), (2) I am starting this install from a fresh 32-bit Desktop Ubuntu 10.04 install (so do not know if there are any issues with other software one might have installed on a Linux box if a problem comes up), and (3) the procedure comes out of the current lack of an Ubuntu binary currently listed as available (as of 6 April 2013) from the LAMMPS website (lammps.sandia.gov/download.html#ubuntu). If (3) changes and is available in an MPI form, what's below will hopefully be unnecessary.

Building Trouble And Solutions

My initial "just unzip, untar, and make linux" attempt on a fresh 10.04 install produced the following error (which I'm reproducing in the expectation that you found this page by typing one of the errors below into a search engine, so you'll find the error and the solutions). NOTE: I build all my programs in /opt for organizational purposes (so replace accordingly):

user@machine:/opt/lammps-3Apr13/src$ sudo make linux

make[1]: Entering directory `/opt/lammps-3Apr13/src/Obj_linux'
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_restart.cpp > write_restart.d
/bin/sh: icc: not found
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_data.cpp > write_data.d
/bin/sh: icc: not found
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../verlet.cpp > verlet.d
/bin/sh: icc: not found
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../velocity.cpp > velocity.d
/bin/sh: icc: not found
...
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../angle_charmm.cpp > angle_charmm.d
/bin/sh: icc: not found
icc -O  -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -c ../angle_charmm.cpp
make[1]: icc: Command not found
make[1]: *** [angle_charmm.o] Error 127
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'
make: *** [linux] Error 2

Obviously, problem Number 1 is the lack of the Intel C Compiler (icc). My solution to this was to download the non-commercial version of the Intel C++ Composer XE for Linux (then I grabbed the Intel Fortran Composer XE for Linux because, well, why not?) currently available from software.intel.com/en-us/non-commercial-software-development (which means this link may be subject to change, so search for "intel c++ noncommercial" in the event).

Unzipping, untaring, and running ./install.sh will, on a fresh Ubuntu install, give you errors that g++ and a proper Java runtime environment are not available on the computer (as part of the pre-requisite search). This is easily solved before the Intel installs by the following (one of which is needed for LAMMPS anyway). I specifically chose the openJDK, but Java 6 or 7 should also do.

sudo apt-get install build-essential openjdk-6-*

After these installs, both Intel Composers should install just fine. If you're installing LAMMPS into a directory that you, the user, has access to, then adding /opt/intel/bin to your PATH will provide you no compiler errors (related to location). If you attempt to install LAMMPS in a directory you, the user, do not have access to, you have to run the install with sudo, which then doesn't likely have the /opt/intel/bin directory in the root PATH, in which case the solution is simply to add a symbolic link for icc into /user/local/bin.

sudo ln -s /opt/intel/bin/icc /usr/local/bin

With icc accessible, running another sudo make linux produces the following errors:

sudo make clean-all
sudo make linux

make[1]: Entering directory `/opt/lammps-3Apr13/src/Obj_linux'
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_restart.cpp > write_restart.d
../write_restart.cpp(15): catastrophic error: cannot open source file "mpi.h"
  #include "mpi.h"
                  ^

icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_data.cpp > write_data.d
../write_data.cpp(15): catastrophic error: cannot open source file "mpi.h"
  #include "mpi.h"
                  ^
...

icc -O  -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -c ../angle_charmm.cpp
../pointers.h(25): catastrophic error: cannot open source file "mpi.h"
  #include "mpi.h"
                  ^

compilation aborted for ../angle_charmm.cpp (code 4)
make[1]: *** [angle_charmm.o] Error 4
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'
make: *** [linux] Error 2

The new problem is now an MPI problem, requiring the installation of (as recommended from the LAMMPS linux Makefile) MPICH. Reading the Makefile (you mean you didn't check this first?) also indicates the need for FFTW2. We can install all of the needed files in one shot with apt-get (and I include build-essential here for completeness, as you either did or didn't install it while trying to solve the icc problem above).

sudo apt-get install build-essential mpich-bin libmpich1.0-dev mpi-doc fftw2 fftw-dev libxaw7-dev libmpich2-dev

This still does not solve the mpi.h issue above, which is a problem with the settings in Makefile.linux (which, apparently, are not Ubuntu-compatible). The solution is, and this is why this is Part 1, to change Makefile.linux to make it compatible with the mpicc compiler in Ubuntu (I will attempt to get it working with icc next). The tweak to my Makefile.linux is provided below (an amalgam of some other Makefile settings. Comment out or delete what's there and add the sections without the "#" to the file):

#######################################################################
## My modified settings are below:

CC = mpicxx
CCFLAGS = -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK
DEPFLAGS =	-M

LINK = $(CC)
LINKFLAGS = -O
SIZE = size

USRLIB = -lfftw

ARCHIVE =	ar
ARFLAGS =	-rc

#######################################################################
## Comment the following out or delete them:

# CC =		icc
# CCFLAGS =	-O
# SHFLAGS =	-fPIC
# DEPFLAGS =	-M

# LINK =		icc
# LINKFLAGS =	-O
# LIB =           -lstdc++
# SIZE =		size

# ARCHIVE =	ar
# ARFLAGS =	-rc
# SHLIBFLAGS =	-shared

I will say that, in some of my searches, I found reference to the use of USRLIB -lmpi. If this is included in the Makefile.linux, you will get the following error upon mpicc (MPICH2) compilation:

/usr/bin/ld: cannot find -lmpl
collect2: ld returned 1 exit status
make[1]: *** [../lmp_linux] Error 1
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'
make: *** [linux] Error 2

So, don't include -lmpi.

With the above Makefile modifications, building of LAMMPS seems to go quite well until the following error is produced:

mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK  -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -c ../dump_dcd.cpp
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK  -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -c ../dump_image.cpp
../dump_image.cpp:32:21: error: jpeglib.h: No such file or directory
../dump_image.cpp: In member function ‘virtual int LAMMPS_NS::DumpImage::modify_param(int, char**)':
../dump_image.cpp:904: warning: suggest parentheses around assignment used as truth value
../dump_image.cpp:911: warning: suggest parentheses around assignment used as truth value
../dump_image.cpp:964: warning: suggest parentheses around assignment used as truth value
../dump_image.cpp:971: warning: suggest parentheses around assignment used as truth value
../dump_image.cpp: In member function ‘void LAMMPS_NS::DumpImage::create_image()':
../dump_image.cpp:611: warning: ‘diameter' may be used uninitialized in this function
../dump_image.cpp:612: warning: ‘color' may be used uninitialized in this function
../dump_image.cpp:612: warning: ‘color1' may be used uninitialized in this function
../dump_image.cpp:612: warning: ‘color2' may be used uninitialized in this function
make[1]: *** [dump_image.o] Error 1
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'
make: *** [linux] Error 2

The jpeglib.h error can likely be solved by installing only one of the libraries below, but I didn't bother to identify which one, instead indiscriminately installing a whole set based on the recommendation of dev.xonotic.org/projects/xonotic/wiki/Repository_Access (having found this link at forums.xonotic.org/showthread.php?tid=1252 – but I removed some of the install that I'm sure was not needed):

sudo apt-get install libxxf86dga-dev libxcb-xf86dri0-dev libxpm-dev libxxf86vm-dev libsdl1.2-dev libsdl-image1.2-dev libclalsadrv-dev libasound2-dev libxext-dev

Finally, a successful build!

make[1]: Entering directory `/opt/lammps-3Apr13/src/Obj_linux'
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_restart.cpp > write_restart.d
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_data.cpp > write_data.d
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../verlet.cpp > verlet.d
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../velocity.cpp > velocity.d
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../variable.cpp > variable.d
...
write_data.o write_restart.o  -lmpich -lpthread -lfftw -ljpeg   -o ../lmp_linux
size ../lmp_linux
   text	   data	    bss	    dec	    hex	filename
3654398	   6928	    264	3661590	 37df16	../lmp_linux
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'

At this point, you can move the lmp_linux executable anywhere (or, as I find myself doing, just keep it in the lammps-DATE/src folder for when you perform subsequent builds).

Running An MPI Calculations

If you've never run through an MPI calculation, you'll get the following errors when you first try to run lmp_linux:

cannot connect to local mpd (/tmp/mpd2.console_user); possible causes:
  1. no mpd is running on this host
  2. an mpd is running but was started without a "console" (-n option)
In case 1, you can start an mpd on this host with:
    mpd &
and you will be able to run jobs just on this host.
For more details on starting mpds on a set of hosts, see
the MPICH2 Installation Guide.

**********

user@machine:/opt/lammps-3Apr13/src$ mpd &

configuration file /home/damianallis/.mpd.conf not found
A file named .mpd.conf file must be present in the user's home
directory (/etc/mpd.conf if root) with read and write access
only for the user, and must contain at least a line with:
MPD_SECRETWORD=
One way to safely create this file is to do the following:
  cd $HOME
  touch .mpd.conf
  chmod 600 .mpd.conf
and then use an editor to insert a line like
  MPD_SECRETWORD=mr45-j9z
into the file.  (Of course use some other secret word than mr45-j9z.)

[1]+  Exit 255                mpd

Simply follow the instructions to put a .mdp.conf in your ~/ folder, start mpd with "mpd &," and run LAMMPS with the following command below (which uses 2 cores (-np 2)).

NOTE: My LAMMPS test (being brand new to it) was to run the first test available from icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_Help. Following the instructions therein (DOWNLOAD: Al99.eam.alloy (780 KB) and calc_fcc.in (1 KB)):

sudo mpirun -np 2 ./lmp_linux < calc_fcc.in

Which should produce the following output:

LAMMPS (3 Apr 2013)
Lattice spacing in x,y,z = 4 4 4
Created orthogonal box = (0 0 0) to (4 4 4)
  1 by 1 by 2 MPI processor grid
Lattice spacing in x,y,z = 4 4 4
Created 4 atoms
Replicating atoms ...
  orthogonal box = (0 0 0) to (4 4 4)
  1 by 1 by 2 MPI processor grid
  4 atoms
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
Memory usage per processor = 2.40372 Mbytes
Step PotEng Lx Ly Lz Press Pxx Pyy Pzz eatoms 
       0   -13.417787            4            4            4     29590.11     29590.11     29590.11     29590.11   -13.417787 
      10   -13.439104         4.04         4.04         4.04    5853.9553    5853.9553    5853.9553    5853.9553   -13.439104 
      14       -13.44         4.05         4.05         4.05     2.726913     2.726913     2.726913     2.726913       -13.44 
Loop time of 0.0287241 on 2 procs for 14 steps with 4 atoms

Minimization stats:
  Stopping criterion = linesearch alpha is zero
  Energy initial, next-to-last, final = 
        -13.4177872966     -13.4399999525     -13.4399999525
  Force two-norm initial, final = 3.54599 0.000335006
  Force max component initial, final = 3.54599 0.000335006
  Final line search alpha, max atom move = 0.0625 2.09379e-05
  Iterations, force evaluations = 14 19

Pair  time (%) = 0.00206506 (7.18931)
Neigh time (%) = 0 (0)
Comm  time (%) = 0.00481999 (16.7803)
Outpt time (%) = 0.000162005 (0.564006)
Other time (%) = 0.021677 (75.4664)

Nlocal:    2 ave 2 max 2 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost:    603 ave 603 max 603 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs:    140 ave 162 max 118 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 280
Ave neighs/atom = 70
Neighbor list builds = 0
Dangerous builds = 0
Total energy (eV) = -13.439999952539944061;
Number of atoms = 4;
Lattice constant (Angstoms) = 4.049999999999998046;
Cohesive energy (eV) = -3.3599999881349860154;
All done!

Brief Update: Amber 11 And AmberTools 1.5 In Ubuntu 12.04 LTS

This post is a brief update to a much longer and more involved discussion of Amber 11 and AmberTools installation in Ubuntu 10.04 LTS (Lucid Lynx) (as the changes are minor and the parallelization setup remains largely the same). You can find this more involved discussion at www.somewhereville.com/?p=1422.

Long/Short – the installation under Ubuntu 12.04 LTS (Precise Pangolin) is not much different and goes without hitch provided you keep your locations organized. NOTE 1: I've not a copy of Amber12, so cannot speak for any changes to its installation procedure. NOTE 2: This install assumes 32-bit only.

Updated Procedure

If you tried installing all of the build software from the 10.04 LTS post, you'll receive errors like the following (as usual, I include error messages for those who are searching against error messages)…

user@machine:~$ sudo apt-get install build-essential cmake doxygen freeglut3-dev g++-multilib gcc-multilib gettext gnuplot ia32-libs lib32asound2 lib32gcc1 lib32gcc1-dbg lib32gfortran3 lib32gomp1 lib32mudflap0 lib32ncurses5 lib32nss-mdns lib32z1 libavdevice52 libc6-dev-i386 libc6-i386 libfreeimage-dev libglew1.5-dev libopenal1 libopenexr-dev libpng12-dev libqt4-dev libssl-dev libstdc++6-4.3-dbg libstdc++6-4.3-dev libstdc++6-4.3-doc libxi-dev libxml-simple-perl libxmu-dev mercurial nfs-common nfs-kernel-server portmap python2.6-dev rpm ssh

Errors…

Reading package lists... Done
Building dependency tree       
Reading state information... Done
Note, selecting 'rpcbind' instead of 'portmap'
Package libc6-i386 is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
However the following packages replace it:
  libc6

Package libstdc++6-4.3-dbg is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

Package libstdc++6-4.3-doc is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

...

Package lib32nss-mdns is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'ia32-libs' has no installation candidate
E: Package 'lib32asound2' has no installation candidate
E: Package 'lib32gcc1' has no installation candidate
E: Package 'lib32gcc1-dbg' has no installation candidate
E: Package 'lib32gfortran3' has no installation candidate
E: Package 'lib32gomp1' has no installation candidate
E: Package 'lib32mudflap0' has no installation candidate
E: Package 'lib32ncurses5' has no installation candidate
E: Package 'lib32nss-mdns' has no installation candidate
E: Package 'lib32z1' has no installation candidate
E: Unable to locate package libavdevice52
E: Package 'libc6-dev-i386' has no installation candidate
E: Package 'libc6-i386' has no installation candidate
E: Package 'libstdc++6-4.3-dbg' has no installation candidate
E: Package 'libstdc++6-4.3-dev' has no installation candidate
E: Package 'libstdc++6-4.3-doc' has no installation candidate
E: Unable to locate package python2.6-dev
E: Couldn't find any package by regex 'python2.6-dev'

The actual install list is smaller than above (reproduced below) to install the necessary additionals to the base 12.04 LTS install. The procedure begins with an aptitude install, update, and upgrade (perform or do not perform as you like).

administrator@ChemistryLab:~$ sudo apt-get install aptitude
administrator@ChemistryLab:~$ sudo aptitude update
administrator@ChemistryLab:~$ sudo aptitude upgrade
administrator@ChemistryLab:~$ sudo apt-get install build-essential cmake doxygen freeglut3-dev g++-multilib gcc-multilib gettext gnuplot ia32-libs bison csh flex fort77 g++ gcc gfortran libbz2-dev libnetcdf-dev libopenmpi-dev libxext-dev libxt-dev openmpi-bin patch tcsh xorg-dev zlib1g-dev fftw-dev 

Amber11 and AmberTools 1.5 Install Specifics

Those used to sudo'ing everything will run into a compile complication with Amber11 as the $AMBERHOME assignment is not carried over into the make serial step:

make[1]: Entering directory `/opt/amber11/AmberTools/src/mmpbsa_py'
/bin/bash setup.sh
AMBERHOME is not set.  Assuming it is /opt/amber11
 Using AmberTools' python
Error importing MMPBSA python modules! MMPBSA.py will not work.
make[1]: *** [install] Error 1
make[1]: Leaving directory `/opt/amber11/AmberTools/src/mmpbsa_py'
make: *** [serial] Error 2

This is an avoidable annoyance by simply building in your $HOME directory and copying the resulting ~/amber11 folder to your desired location (and setting $PATH statements accordingly).

AmberTools 1.5 Install

Procedure is as found in the previous post (I am assuming that the files are sitting in your $HOME (cd ~/) fold…

tar xjf AmberTools-1.5.tar.bz2
cd amber11/
echo "export AMBERHOME=$PWD" >> ~/.bashrc
echo "export PATH=$PATH:$AMBERHOME/bin" >> ~/.bashrc
source ~/.bashrc
wget http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all
patch -p0 < bugfix.all
rm bugfix.all
cd AmberTools/src/
./configure gnu
make install

The Amber11 install is made slightly different than the previous instruction set by the download of the bugfix.all.tar.bz2 file and the different run of apply_bugfix.x. For a serial install...

tar xfj Amber11.tar.bz2
cd ~/
wget http://ambermd.org/bugfixes/11.0/bugfix.all.tar.bz2
wget http://ambermd.org/bugfixes/11.0/apply_bugfix.x
chmod +x ./apply_bugfix.x
./apply_bugfix.x bugfix.all.tar.bz2

You'll get a few CUDA-specific errors during the bugfix. I skipped the last two patches as I'm not compiling a CUDA-specific version.

cd AmberTools/src/
./configure gnu
cd $AMBERHOME
./AT15_Amber11.py
cd src/
make serial

With this completed, move the amber11 folder to /opt (or wherever), modify your .bashrc, and run the tests.

cd ~/
sudo mv amber11 /opt
nano .bashrc

Place the following into the .bashrc file

export AMBERHOME=/opt/amber11

And run the tests…

cd /opt/amber11/test/
make -f Makefile