diff --git a/README.md b/README.md
index 32091a9364a52a70985abe288b50bfcc47d53d54..7c76215207038b458f0511ba145680f36dd1d960 100644
--- a/README.md
+++ b/README.md
@@ -1,17 +1,22 @@
-# cell_algorithms
+# NestMC Prototype
+
+This is the repository for the NestMC prototype code. Unfortunately we do not have thorough documentation of how-to guides.
+Below are some guides for how to build the project and run the miniapp.
+Contact us or submit a ticket if you have any questions or want help.
```bash
# clone repo
-git clone git@github.com:eth-cscs/cell_algorithms.git
-cd cell_algorithms/
+git clone git@github.com:eth-cscs/nestmc-proto.git
+cd nestmc-proto/
# setup sub modules
git submodule init
git submodule update
# setup environment
-# on a desktop system this might not be required
-# on a cluster this could be required
+# on a desktop system this is probably not required
+# on a cluster this is usually required to make sure that an appropriate
+# compiler is chosen.
module load gcc
module load cmake
export CC=`which gcc`
@@ -31,8 +36,7 @@ cd tests
## MPI
Set the `WITH_MPI` option either via the ccmake interface, or via the command line as shown below.
-For the time being our CMake configuration does not try to detect MPI.
-Instead, it relies on the user specifying an MPI wrapper for the compiler by setting the `CXX` and `CC` environment variables.
+To ensure that CMake detects MPI correctly, you should specify the MPI wrapper for the compiler by setting the `CXX` and `CC` environment variables.
```
export CXX=mpicxx
@@ -47,7 +51,6 @@ Support for multi-threading requires Intel Threading Building Blocks (TBB).
When TBB is installed, it comes with some scripts that can be run to set up the user environment.
The scripts set the `TBB_ROOT` environment variable, which is used by the CMake configuration to find TBB.
-
```
source <path to TBB installation>/tbbvars.sh
cmake <path to CMakeLists.txt> -DWITH_TBB=ON
@@ -56,6 +59,9 @@ cmake <path to CMakeLists.txt> -DWITH_TBB=ON
### TBB on Cray systems
To compile with TBB on Cray systems, load the intel module, which will automatically configure the environment.
+The guide below shows how to use the version of TBB that is installed as part of the Intel compiler toolchain.
+It is recommended that you install the most recent version of TBB yourself, and link against this, because older versions
+of TBB don't work with recent versions of GCC.
```
# load the gnu environment for compiling the application
@@ -80,7 +86,7 @@ cmake <path to CMakeLists.txt> -DWITH_TBB=ON -DWITH_MPI=ON -DSYSTEM_CRAY=ON
# targetting KNL
-## build modparser
+## build modparser
The source to source compiler "modparser" that generates the C++/CUDA kernels for the ion channels and synapses is in a separate repository.
It is included in our project as a git submodule, and by default it will be built with the same compiler and flags that are used to build the miniapp and tests.
@@ -116,8 +122,8 @@ which modcc
```bash
# clone the repo and set up the submodules
-git clone TODO
-cd cell_algorithms
+git clone https://github.com/eth-cscs/nestmc-proto.git
+cd nestmc-proto
git submodule init
git submodule update
@@ -127,13 +133,6 @@ cd build_knl
## build miniapp
-# clone the repo and set up the submodules
-git clone https://github.com/bcumming/cell_algorithms.git
-cd cell_algorithms
-
-# checkout the knl branch
-git checkout knl
-
# setup submodules
git submodule init
git submodule update
diff --git a/mechanisms/mod/exp2syn.mod b/mechanisms/mod/exp2syn.mod
old mode 100755
new mode 100644
index ea0cf025e9228216b4699161a2e574ca1d1dda6e..591fcbca8aff2779cc36286b554d6d17d9f475c1
--- a/mechanisms/mod/exp2syn.mod
+++ b/mechanisms/mod/exp2syn.mod
@@ -1,50 +1,47 @@
NEURON {
- POINT_PROCESS exp2syn
- RANGE tau1, tau2, e
- NONSPECIFIC_CURRENT i
+ POINT_PROCESS exp2syn
+ RANGE tau1, tau2, e
+ NONSPECIFIC_CURRENT i
}
UNITS {
- (nA) = (nanoamp)
- (mV) = (millivolt)
- (uS) = (microsiemens)
+ (mV) = (millivolt)
}
PARAMETER {
- tau1 = .5 (ms) : <1e-9,1e9>
- tau2 = 2 (ms) : <1e-9,1e9>
- e=0 (mV)
+ tau1 = 0.5 (ms)
+ tau2 = 2 (ms)
+ e = 0 (mV)
}
ASSIGNED {
- factor
+ factor
}
STATE {
- A : (uS)
- B : (uS)
+ A B
}
INITIAL {
- LOCAL tp
- A = 0
- B = 0
- tp = (tau1*tau2)/(tau2 - tau1) * log(tau2/tau1)
- factor = -exp(-tp/tau1) + exp(-tp/tau2)
- factor = 1/factor
+ LOCAL tp
+ A = 0
+ B = 0
+ tp = (tau1*tau2)/(tau2 - tau1) * log(tau2/tau1)
+ factor = 1 / (-exp(-tp/tau1) + exp(-tp/tau2))
}
BREAKPOINT {
- SOLVE state METHOD cnexp
- i = (B - A)*(v - e)
+ SOLVE state METHOD cnexp
+ i = (B - A)*(v - e)
}
DERIVATIVE state {
- A' = -A/tau1
- B' = -B/tau2
+ A' = -A/tau1
+ B' = -B/tau2
}
NET_RECEIVE(weight) {
- A = A + weight*factor
- B = B + weight*factor
+ A = A + weight*factor
+ B = B + weight*factor
}
+
diff --git a/mechanisms/mod/expsyn.mod b/mechanisms/mod/expsyn.mod
index 16d10c5cf856cd87e50252dca2163d844588e2b9..44da3697ddf01321ea9ee5991791baa0f0145880 100644
--- a/mechanisms/mod/expsyn.mod
+++ b/mechanisms/mod/expsyn.mod
@@ -5,22 +5,18 @@ NEURON {
}
UNITS {
- (nA) = (nanoamp)
(mV) = (millivolt)
- (uS) = (microsiemens)
}
PARAMETER {
- : the default for Neuron is 0.1
- :tau = 0.1 (ms) : <1e-9,1e9>
- tau = 2.0 (ms) : <1e-9,1e9>
+ tau = 2.0 (ms) : the default for Neuron is 0.1
e = 0 (mV)
}
ASSIGNED {}
STATE {
- g : (uS)
+ g
}
INITIAL {
@@ -39,3 +35,4 @@ DERIVATIVE state {
NET_RECEIVE(weight) {
g = g + weight
}
+
diff --git a/mechanisms/mod/hh.mod b/mechanisms/mod/hh.mod
index 8b23f44a4dc3e27cdbb2d78a161b9504c8651073..f5acc9fc7c66d283d170f5b11d1ba2da21e039fa 100644
--- a/mechanisms/mod/hh.mod
+++ b/mechanisms/mod/hh.mod
@@ -1,24 +1,3 @@
-TITLE hh.mod squid sodium, potassium, and leak channels
-
-: COMMENT
-: This is the original Hodgkin-Huxley treatment for the set of sodium,
-: potassium, and leakage channels found in the squid giant axon membrane.
-: ("A quantitative description of membrane current and its application
-: conduction and excitation in nerve" J.Physiol. (Lond.) 117:500-544 (1952).)
-: Membrane voltage is in absolute mV and has been reversed in polarity
-: from the original HH convention and shifted to reflect a resting potential
-: of -65 mV.
-: Remember to set celsius=6.3 (or whatever) in your HOC file.
-: See squid.hoc for an example of a simulation using this model.
-: SW Jaslove 6 March, 1992
-: ENDCOMMENT
-
-UNITS {
- (mA) = (milliamp)
- (mV) = (millivolt)
- (S) = (siemens)
-}
-
NEURON {
SUFFIX hh
USEION na READ ena WRITE ina
@@ -28,13 +7,17 @@ NEURON {
GLOBAL minf, hinf, ninf, mtau, htau, ntau
}
+UNITS {
+ (mV) = (millivolt)
+ (S) = (siemens)
+}
+
PARAMETER {
- gnabar = .12 (S/cm2) : <0,1e9>
- gkbar = .036 (S/cm2) : <0,1e9>
- gl = .0003 (S/cm2) : <0,1e9>
+ gnabar = .12 (S/cm2)
+ gkbar = .036 (S/cm2)
+ gl = .0003 (S/cm2)
el = -54.3 (mV)
celsius = 6.3 (degC)
- :celsius = 37 (degC)
}
STATE {
@@ -77,7 +60,7 @@ DERIVATIVE states {
n' = (ninf-n)/ntau
}
-PROCEDURE rates(v) :(mV))
+PROCEDURE rates(v)
{
LOCAL alpha, beta, sum, q10
@@ -105,21 +88,13 @@ PROCEDURE rates(v) :(mV))
ninf = alpha/sum
}
+: We don't trap for zero in the denominator like Neuron, because function
+: inlining in modparser won't support it. There is a good argument that
+: vtrap should be provided as a built in of the language, because
+: - it is a common pattern in many mechanisms.
+: - it can be implemented efficiently on different back ends if the
+: compiler has enough information.
FUNCTION vtrap(x,y) {
- : Traps for 0 in denominator of rate eqns.
-
- : Disabled for function inlining...
- : there is a very good case for making vtrap a builtin function for the language
- : - it is ubiquitous: used in so many models of ion channels
- : - platform specific optimizations written in assembly/intrinsics
- : required to facilitate vectorization/minimize branch misses
-
- :if (fabs(x/y) < 1e-6) {
- : vtrap = y*(1 - x/y/2)
- :}else{
- : vtrap = x/(exp(x/y) - 1)
- :}
-
vtrap = x/(exp(x/y) - 1)
}
diff --git a/mechanisms/mod/pas.mod b/mechanisms/mod/pas.mod
index b7dc2ad6d2a343bb2333c5b8ecfec17060150865..6653f34e1bf3a0b53f367c826f2d424ca7f86927 100644
--- a/mechanisms/mod/pas.mod
+++ b/mechanisms/mod/pas.mod
@@ -1,8 +1,5 @@
-TITLE passive membrane channel
-
UNITS {
(mV) = (millivolt)
- (mA) = (milliamp)
(S) = (siemens)
}
@@ -15,8 +12,8 @@ NEURON {
INITIAL {}
PARAMETER {
- g = .001 (S/cm2) :<0,1e9>
- e = -65 (mV) : we use -65 for the ball and stick model, instead of Neuron default of -70
+ g = .001 (S/cm2)
+ e = -65 (mV) : we use -65 for the ball and stick model, instead of Neuron default of -70
}
ASSIGNED {