init this repo

2020-10-12 15:38:02 -05:00
commit 6c332e722a
76 changed files with 1114 additions and 0 deletions
--- a/pages/work/alcap.txt
+++ b/pages/work/alcap.txt
@@ -0,0 +1 @@
+AlCap experiment notes
--- a/pages/work/alcap/r15a-xray-on-mu2e.bu.edu.txt
+++ b/pages/work/alcap/r15a-xray-on-mu2e.bu.edu.txt
@@ -0,0 +1,141 @@
+This note describe how I set up the Cocalc server on ''mu2e.bu.edu'' machine
+====== Docker services ======
+===== Linuxserver swag =====
+This service takes care of Let's Encrypt certificate issuance and renewal. Be careful though, do not delete/recreate this service too often because there is a rate limit of 5 certs per week.
+  * ports ''80'', ''443'', and ''8443'' are exposed. The first two are needed for the certificates, the ''8443'' is for the Cocalc service
+  * nice thing about ''linuxserver'' dockers are graceful handling of ''uid'' and ''gid''
+  * asking for certificate for ''mu2e.bu.edu'' only. Cocalc doesn't appear to work nicely with a subfolder path. And subdomain doesn't appear to work on this box (maybe net admin at BU must add/allow subdomain?).
+<code yaml>
+  swag:
+    image: linuxserver/swag
+    container_name: swag
+    cap_add:
+      - NET_ADMIN
+    environment:
+      - PUID=1004
+      - PGID=1004
+      - TZ=America/New_York
+      - URL=mu2e.bu.edu
+      - VALIDATION=http
+      - ONLY_SUBDOMAINS=false #optional
+      - STAGING=false
+    volumes:
+      - ./swag-config:/config
+    ports:
+      - 443:443
+      - 80:80 #optional
+      - 0.0.0.0:8443:8443
+    restart: unless-stopped
+    networks:
+      - cocalc
+
+</code>
+===== Cocalc service =====
+Copied from Cocalc documentation, nothing much to say here.
+<code yaml>
+  cocalc:
+    image: sagemathinc/cocalc
+    container_name: cocalc
+    volumes:
+      - ./cocalc-data:/projects
+    # ports:
+    #   - 0.0.0.0:8752:443
+    restart: unless-stopped
+    networks:
+      - cocalc
+</code> 
+
+====== Further configuration ======
+===== Reverse proxy for Cocalc =====
+The proxy is configured in ''swag'' by adding a server on port ''8443'' which is forwarded to ''cocalc:443''.
+<code nginx>
+(base) @mu2e:cocalc-docker nam $ cat swag-config/nginx/proxy-confs/cocalc.subdomain.conf 
+server {
+        listen 8443 ssl;
+        listen [::]:8443 ssl;
+
+        index index.html index.htm index.php;
+
+        server_name mu2e.bu.edu;
+
+        # all ssl related config moved to ssl.conf
+        include /config/nginx/ssl.conf;
+  client_max_body_size 50;
+  server_tokens off;
+
+   location / {
+       proxy_pass https://cocalc:443;
+       proxy_http_version 1.1;
+       proxy_set_header Upgrade $http_upgrade;
+       proxy_set_header Connection "upgrade";
+       proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+
+       proxy_set_header X-Forwarded-Proto $scheme;
+       proxy_read_timeout 3m;
+       proxy_send_timeout 3m;
+   }
+}
+</code>
+===== Spin it up! =====
+Run ''docker-compose up -d''
+
+===== Configure user on Cocalc =====
+  * self-register on first launch
+  * launch an interactive shell within running ''cocalc'' container, 
+  * generate SSH pubkey and add to Github
+  * create ''.gitconfig''
+    <code bash>
+    ~$ cat .gitconfig 
+    [user]
+            name = Nam Tran
+            email = thnam.me@gmail.com
+    [core]
+            editor = vim
+            quotepath = false
+            autocrlf = input
+            excludesfile = /projects/0223d4fc-683f-424a-8bdf-8d867a4ac9c9/.gitexcludes
+    [merge]
+            tool = opendiff
+            conflictstyle = diff3
+
+    [alias]
+            ci = commit
+            co = checkout
+            st = status
+            br = branch
+            hist = log --pretty=format:\"%h %ad | %s%d [%an]\" --graph --date=short
+            type = cat-file -t
+            dump = cat-file -p
+            ignored = !git ls-files -v | grep ^[[:lower:]]
+
+    [color]
+            ui = true
+    [push]
+            default = tracking
+    [branch]
+            autosetupmerge = true
+    </code>
+===== Prepare Latex code =====
+  * Pull the source ''~$ git clone git@github.com:bostonu-cas/r15a_xray.git''
+  * Install Revtex v4.2 <code bash>
+    ~$ mkdir texmf
+    ~$ cd texmf/
+    ~$ wget https://journals.aps.org/revtex/revtex4-2-tds.zip
+    ~$ unzip revtex4-2-tds.zip 
+    </code>
+  * Go to the source directory, Cocalc automatically runs ''latexmk'' to compile
+===== Syncing =====
+  * Automatic pull <code bash>
+    ~$ mkdir utils && cd utils && git clone https://github.com/kolbasa/git-repo-watcher
+    # Add PATH, then run in a latex terminal
+    ~/r15a_xray$ git-repo-watcher -d . -i 60 > /dev/null 2>&1 &
+    </code>
+  * Auto commit and push
+    * prepare script and add to ''PATH'' <code bash>
+    ~$ cat utils/git-auto-commit 
+    #!/usr/bin/env bash
+    script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+    git pull && git ci -am "auto-commit from mu2e.bu.edu:8443" && git push
+    </code>
+    * edit compile command to: ''latexmk -pdf ... xray.tex && ~/utils/git-auto-commit''
--- a/pages/work/gm2.txt
+++ b/pages/work/gm2.txt
@@ -0,0 +1,2 @@
+G-2 related notes
+  * [[work:gm2:esq|ESQ]]
--- a/pages/work/gm2/esq.txt
+++ b/pages/work/gm2/esq.txt
@@ -0,0 +1,3 @@
+Electrostatic quadrupole
+  * [[work:gm2:esq:bu_controller|BU controller]]
+      * [[work:gm2:esq:bu_controller:compiling_on_opt|Test compiling on opt]]
--- a/pages/work/gm2/esq/bu_controller.txt
+++ b/pages/work/gm2/esq/bu_controller.txt
@@ -0,0 +1 @@
+{{indexmenu>work:gm2:esq:bu_controller}}
--- a/pages/work/gm2/esq/bu_controller/bu_controller_manual.txt
+++ b/pages/work/gm2/esq/bu_controller/bu_controller_manual.txt
@@ -0,0 +1,51 @@
+====== Hardware ======
+===== Overview =====
+The box's job is to emit TTL pulses to control 4 HV pulsers, and stop doing so when a trouble is detected.
+===== Block diagram and photo =====
+{{work:gm2:esq:bu_controller:bu_controller_block_diagram.png?800x0}}
+===== Carrier board =====
+The carrier board has a PicoZed System-On-Module (SOM), which contains:
+  * a XC7Z020 System-on-Chip (one dual core ARM processor, and one Artix-7 FPGA)
+  * 1 GB of DDR3 SDRAM
+  * 16 GB eMMC memory
+  * Ethernet interface
+  * UART interface
+
+This board serves as a bridge between user and programmable logic parts (ADC boards) of the controller.
+There is a Linux system (Xilin Petalinux 2015.4) installed:
+  * user: ''root''
+  * password: ''root''
+  * static IP address: ''192.168.30.89''
+===== ADC boards =====
+There are 4 identical ADC boards in the box, each has one pulser and one 8-channel waveform digitizer.
+{{work:gm2:esq:bu_controller:bu_controller_front_panel.png?800x0}}
+==== Pulser ====
+{{work:gm2:esq:bu_controller:io_numbering.png?600x0}}
+
+Each pulser has 8 SMA outputs, numbered from 1 to 8 from left to right:
+  * outputs 1-4: RF control outputs
+  * output 5: discharge signal
+  * output 6: charge signal, first step
+  * output 7: charge signal, second step for two-step HV cabinets. Not used in case of 1-step pulser.
+  * outputs 8: spare I/O
+
+Pulse modes are:
+  - External trigger: produces a set of pulse after receiving a LVTTL (3.3 V) logic pulse at the external trigger input. The trigger pulse width should not exceed 50 ns.
+  - Internal trigger: produces sets of pulses periodically, up to 100 Hz
+
+==== WFD ====
+These are 12-bit WFDs, run at 100 MSPS. Clock source can be either an external 40 MHz clock, or internal clock generated by the carrier board.
+
+The WFD inputs are numbered from 1 to 8 from left to right, similar to the pulser numbering above. These inputs have protection against surges might happen during a spark.
+
+The WFDs provide several pieces of information:
+  * waveforms: all channels are in zero-suppressed mode, which will only export samples above programmed individual threshold. The maximum sampling length is 100 us (the current firmware can only give 20 us) 
+  * spark threshold (not the waveform threshold above) crossings: there are upper and lower thersholds for each channel, the threshold crossing counting is active for the whole g-2 muon fill (~700 us)
+  * waveform integrals at charge and discharge times: the integration starts at charge and discharge steps, maximum integration length is 256 samples (~2.5 us)
+
+Each WFD will produce one block of data for one trigger, the data format is described here: https://docs.google.com/spreadsheets/d/19r_blWufX368hKRkoa1FGhIzBLOzIvKfg5ZKRVmEVkI/edit?usp=sharing. The data is written to RAM on the carrier board, and can be accessed via a DMA controller.
+
+====== Firmware ======
+====== Software ======
+
+
--- a/pages/work/gm2/esq/bu_controller/carrier_firmware_2020-10-05_issues.txt
+++ b/pages/work/gm2/esq/bu_controller/carrier_firmware_2020-10-05_issues.txt
@@ -0,0 +1,6 @@
+  * Board 3 could not be initialized
+  * Skipping every other pulse (yellow) in the 8 pulses train (teal)
+  {{work:gm2:esq:bu_controller:pxl_20201007_202452451.jpg?400x0}}
+
+  * Switching back to ''2019-12-13'' version fixed both of them
+  {{work:gm2:esq:bu_controller:pxl_20201007_210215108.jpg?400x0}}
--- a/pages/work/gm2/esq/bu_controller/carrier_firmware_2020-10-08_test.txt
+++ b/pages/work/gm2/esq/bu_controller/carrier_firmware_2020-10-08_test.txt
@@ -0,0 +1,48 @@
+====== First test ======
+  * It seems the issue of board initialization is still there, but moves to board 4 ...
+  * Still shows only 4 out of 8 pulses in a train
+  * will try with different triggers
+<code bash>
+daq@gm2-01:scripts $ BUTool -q 192.168.30.89
+Registered device: G2QUAD
+>write TRIGGER.STATUS.ENABLE_PULSERS 1
+Write to register TRIGGER.STATUS.ENABLE_PULSERS
+>write TRIGGER.FREE_RUN.EN_FR_TRIG 0
+Write to register TRIGGER.FREE_RUN.EN_FR_TRIG
+>write TRIGGER.FREE_RUN.EN_EXT_TRIG 1
+Write to register TRIGGER.FREE_RUN.EN_EXT_TRIG
+>read SYSTEM.SYNTH_DATE
+                                 SYSTEM.SYNTH_DATE: 0x20201008
+>read ADCBOARD.1.*SYNTH_DATE
+                      ADCBOARD.1.SYSTEM.SYNTH_DATE: 0x20201005
+>read ADCBOARD.2.*SYNTH_DATE
+                      ADCBOARD.2.SYSTEM.SYNTH_DATE: 0x20201005
+>read ADCBOARD.3.*SYNTH_DATE
+                      ADCBOARD.3.SYSTEM.SYNTH_DATE: 0x20201005
+</code>
+====== Trigger from a waveform generator ======
+  * The function generator is programmed to output a burst of 8 pulses: 3 Vpp, 1.5 V offset, 10 ms separation every 1.4 s. Pulse width is adjustable. This WG has minimum 6 ns rise time and fall time.
+  {{work:gm2:esq:bu_controller:pxl_20201008_190541385.jpg?600x0}}
+  * Output 1 & 2 are in-sync
+  {{work:gm2:esq:bu_controller:pxl_20201008_190526636.jpg?600x0}}
+  * Output 1 is kept on channel 1 of the scope, output 2 goes to the ext. trigger input of the BU controller
+====== Tweaking trigger pulse length ======
+Channel 1 on scope is the synced signal of ext trigger, channel 2 is discharge pulse from ADC board 1.
+
+  * < 50 ns, still shows only 4 pulses. All pulses from 12 ns to 50 ns worked.
+{{work:gm2:esq:bu_controller:pxl_20201008_191532389.jpg}}
+{{work:gm2:esq:bu_controller:pxl_20201008_191547871.jpg}}
+{{work:gm2:esq:bu_controller:pxl_20201008_191643263.jpg}}
+{{work:gm2:esq:bu_controller:pxl_20201008_191710289.jpg}}
+{{work:gm2:esq:bu_controller:pxl_20201008_191730525.jpg}}
+  * 54 ns, picking up random pulses among 8, but never 2 consecutive ones
+{{work:gm2:esq:bu_controller:pxl_20201008_191758570.jpg}}
+{{work:gm2:esq:bu_controller:pxl_20201008_191806670.jpg}}
+{{work:gm2:esq:bu_controller:pxl_20201008_191757168.jpg}}
+  * 56 ns, still can pick up pulses
+{{work:gm2:esq:bu_controller:pxl_20201008_191818632.jpg}}
+{{work:gm2:esq:bu_controller:pxl_20201008_191821833.jpg}}
+  * 60 ns, no trigger picked up at all
+===== Different pulse separation =====
+Still only 4 pulses, there seems to be some change in phase.
+{{work:gm2:esq:bu_controller:pxl_20201008_195535792.jpg}}{{work:gm2:esq:bu_controller:pxl_20201008_195613934.jpg}}{{work:gm2:esq:bu_controller:pxl_20201008_195009724.jpg}}{{work:gm2:esq:bu_controller:pxl_20201008_194714818.jpg}}
--- a/pages/work/gm2/esq/bu_controller/compiling_on_gm2-01.txt
+++ b/pages/work/gm2/esq/bu_controller/compiling_on_gm2-01.txt
@@ -0,0 +1,40 @@
+====== Prepare code ======
+===== Zynq software =====
+<code bash>
+daq@gm2-01:ESQ $ svn co http://gauss.bu.edu/svn/g2-quad-pulser.firmware/carrier zynq-carrier.trunk.svn
+...
+Checked out revision 548.
+daq@gm2-01:zynq-carrier.trunk.svn $ svn log | head
+------------------------------------------------------------------------
+r548 | dgastler | 2020-10-05 15:11:09 -0500 (Mon, 05 Oct 2020) | 1 line
+
+New version for Nam
+------------------------------------------------------------------------
+r546 | dgastler | 2020-10-05 07:52:45 -0500 (Mon, 05 Oct 2020) | 1 line
+
+updated address tables
+------------------------------------------------------------------------
+r545 | dgastler | 2020-10-05 07:17:03 -0500 (Mon, 05 Oct 2020) | 1 line
+</code>
+
+===== Copy old BUTool over =====
+<code bash>
+daq@gm2-01:zynq-carrier.trunk.svn $ cp -r ~/ESQ/zynq-carrier.trunk/os/software/BUTool ./os/software/
+</code>
+
+====== Build ======
+===== BUTool =====
+Clean up old code, regenerate ''env.sh'', then ''make'' again
+<code bash>
+daq@gm2-01:BUTool $ export PLATFORM=petalinux
+daq@gm2-01:BUTool $ ./setup.sh
+env.sh
+Source env.sh and run 'make' to build BUTool
+daq@gm2-01:BUTool $ make clean
+daq@gm2-01:BUTool $ make -j4 && make install
+</code>
+===== Zynq software =====
+Edit the ''buildArm.sh'' a little bit (skip building BUTool since it is done in previous step)
+<code bash>
+daq@gm2-01:software $ ./buildArm.sh
+</code>
--- a/pages/work/gm2/esq/bu_controller/compiling_on_opt.txt
+++ b/pages/work/gm2/esq/bu_controller/compiling_on_opt.txt
@@ -0,0 +1,137 @@
+====== Check out codes ======
+===== Zynq software =====
+<code bash>
+nam@opt:ESQ $ svn co http://gauss.bu.edu/svn/g2-quad-pulser.firmware
+nam@opt:ESQ $ mv g2-quad-pulser.firmware g2-quad-pulser.firmware.svn
+nam@opt:g2-quad-pulser.firmware.svn $ cd carrier/trunk/os/software/
+</code>
+Make sure this is the latest version (as of 2020/10/05):
+<code>
+nam@opt:software $ svn info
+Path: .
+Working Copy Root Path: /home/nam/work/gm2/ESQ/g2-quad-pulser.firmware.svn
+URL: http://gauss.bu.edu/svn/g2-quad-pulser.firmware/carrier/trunk/os/software
+Relative URL: ^/carrier/trunk/os/software
+Repository Root: http://gauss.bu.edu/svn/g2-quad-pulser.firmware
+Repository UUID: 7ce3f3ac-83d5-4068-a32b-ab773f4188fc
+Revision: 548
+Node Kind: directory
+Schedule: normal
+Last Changed Author: dgastler
+Last Changed Rev: 546
+Last Changed Date: 2020-10-05 07:52:45 -0500 (Mon, 05 Oct 2020)
+</code>
+===== BUTool =====
+
+<code bash>
+nam@opt:software $ svn co http://gauss.bu.edu/svn/butool/trunk BUTool
+nam@opt:BUTool $ svn info
+...
+Last Changed Rev: 70
+Last Changed Date: 2019-09-17 10:35:07 -0500 (Tue, 17 Sep 2019)
+</code>
+Need to revert to ''r42'' which is compatible with Petalinux 2015.4
+<code bash>
+nam@opt:BUTool $ svn up -r42
+nam@opt:BUTool $ svn info
+Path: .
+Working Copy Root Path: /home/nam/work/gm2/ESQ/g2-quad-pulser.firmware.svn/carrier/trunk/os/software/BUTool
+URL: http://gauss.bu.edu/svn/butool/trunk
+...
+Last Changed Rev: 42
+Last Changed Date: 2018-07-12 15:56:11 -0500 (Thu, 12 Jul 2018)
+</code>
+
+====== Build ======
+===== BUTool =====
+Run ''setup.sh'' to generate ''env.sh'' where all environment variables would be set. Also change the path to Petalinux to match the local installation.
+<code bash>
+nam@opt:BUTool $ PLATFORM=petalinux ./setup.sh
+env.sh
+Source env.sh and run 'make' to build BUTool
+nam@opt:BUTool $ cat env.sh
+if [[ $_ == $0 ]]; then
+  echo "$0 is meant to be sourced:"
+  echo "  source $0"
+  exit 0
+fi
+
+export PLATFORM="petalinux"
+export PREFIX="/work/butool"
+export MAKEFLAGS="-I /home/nam/work/gm2/ESQ/g2-quad-pulser.firmware.svn/carrier/trunk/os/software/BUTool/mk"
+export PROJECT_ROOT="/home/nam/work/gm2/ESQ/g2-quad-pulser.firmware.svn/carrier/trunk/os/software/BUTool"
+export PATH="$PATH:/work/butool/bin"
+
+export VIVADO_VERSION=2015.4
+export VIVADO_SDK=/home/nam/Downloads/petalinux-v2015.4-final/settings.sh
+
+source $VIVADO_SDK
+
+export CXX=arm-xilinx-linux-gnueabi-g++
+export CC=arm-xilinx-linux-gnueabi-gcc
+
+export CROSS_HOST=arm-xilinx-linux-gnueabi
+
+export MAKEOBJDIRPREFIX="$PROJECT_ROOT/obj"
+export DESTDIR="$PROJECT_ROOT/install"
+
+export BUTOOL_COMPILETIME_PATH="$DESTDIR/$PREFIX"
+export BUTOOL_RUNTIME_PATH="$PREFIX"
+</code>
+Source ''env.sh'' and ''make'':
+<code bash>
+nam@opt:BUTool $ . env.sh
+nam@opt:BUTool $ make
+...
+  CXX (link)  -o obj/lib/libBUTool.so
+  CXX   src/tool/BUTool.cxx
+  CXX (link)  -o obj/bin/BUTool
+</code>
+===== Zynq software =====
+<code bash>
+nam@opt:BUTool $ cd ../
+nam@opt:software $ ./buildArm.sh
+</code>
+Need to change a few things
+<code bash>
+nam@opt:software $ svn diff
+Index: buildArm.sh
+===================================================================
+--- buildArm.sh	(revision 548)
+++ buildArm.sh	(working copy)
+@@ -15,7 +15,7 @@
+ export PLATFORM=petalinux
+
+ cd BUTool
+-./setup.sh
+#./setup.sh
+ source env.sh
+ make clean
+ make
+Index: zynq_daq/Makefile
+===================================================================
+--- zynq_daq/Makefile	(revision 548)
+++ zynq_daq/Makefile	(working copy)
+@@ -1,6 +1,9 @@
+SHELL := /bin/bash
+ VIVADO_VERSION=2015.4
+ #VIVADO_VERSION=2017.2
+ VIVADO_SDK="/opt/Xilinx/SDK/"${VIVADO_VERSION}"/settings64.sh"
+VIVADO_SDK=/home/nam/Downloads/petalinux-v2015.4-final/settings.sh
+
+
+ CXX=source ${VIVADO_SDK} && arm-xilinx-linux-gnueabi-g++
+ #CXXFLAGS+=-c -g -O2 -Wall -Wextra -Werror -Wno-pointer-arith -I ./ -I ${G2FRAME_PREFIX}/include
+Index: zynq_pl_bridge/Makefile
+===================================================================
+--- zynq_pl_bridge/Makefile	(revision 548)
+++ zynq_pl_bridge/Makefile	(working copy)
+@@ -1,6 +1,7 @@
+
+ VIVADO_VERSION=2015.4
+ VIVADO_SDK="/opt/Xilinx/SDK/"$(VIVADO_VERSION)"/settings64.sh"
+VIVADO_SDK=/home/nam/Downloads/petalinux-v2015.4-final/settings.sh
+
+ CXX=source $(VIVADO_SDK) && arm-xilinx-linux-gnueabi-g++
+ CXXFLAGS+=-c -O2 -static -Wall -Wextra -Werror -Wno-pointer-arith
+</code>
--- a/pages/work/gm2/esq/bu_controller/test_with_single_burst_of_8_pulses.txt
+++ b/pages/work/gm2/esq/bu_controller/test_with_single_burst_of_8_pulses.txt
@@ -0,0 +1,3 @@
+- log-01: before
+- log-02: after
+- log-03: another pulse