Re: [stem-dev] Reason why weekly integration won't work on Mac?

["James Kaufman" <jhkauf@xxxxxxxxxx>]

Thank you Emily,
The behavior you observed is definitely
an issue with the new version of Java - but it seems to have been around
for several versions. We'll have to test the e4 build with the latest Java
once it is ready.

Ahmad,
What version of Java are you running
on your dev machine?

Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:      
 Emily Nixon <emily.nixon@xxxxxxxxxxxxx>
To:      
 Stefan Edlund <sedlund@xxxxxxxxxx>,
James Kaufman <jhkauf@xxxxxxxxxx>
Cc:      
 "Ahmad.Swaid@xxxxxxxxxxx"
<Ahmad.Swaid@xxxxxxxxxxx>, "judy.douglas07@xxxxxxxxx" <judy.douglas07@xxxxxxxxx>
Date:      
 07/16/2018 02:33 AM
Subject:    
   Re: Reason why
weekly integration won't work on Mac?

---

Hi all,

Jamie and I found the solution to the problems
I have been experiencing. Jamie identified that we were using different
versions of java. I had the latest version (Version 8 Update 171), whereas
he was using an older version (Version 8 update 144). The new update must
be not compatible in some way with STEM.

To uninstall the new version from my mac,
I used the following commands within my terminal window:

sudo rm -rf /Library/Java/*

sudo rm -rf /Library/PreferencePanes/Java*

sudo rm -rf /Library/Internet\ Plug-Ins/Java*

I then downloaded the jdk and jre for Java Version 8 Update 144 from the Oracle Archive:

http://www.oracle.com/technetwork/java/javase/downloads/java-archive-javase8-2177648.html


I can now confirm that the Weekly Integration Build works on my mac.

This is a good workaround for now. Perhaps it might be worth posting this on the wiki?

Do you think the new version of STEM will be compatible with the new version of Java?

Thanks for all your help with this (especially Jamie!).

Best wishes,

Emily  

Emily Nixon
PhD Student

Demonstrator


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389

---

From: Stefan Edlund <sedlund@xxxxxxxxxx>
Sent: 11 July 2018 22:36:16
To: James Kaufman
Cc: Ahmad.Swaid@xxxxxxxxxxx; Emily Nixon; judy.douglas07@xxxxxxxxx
Subject: Re: Reason why weekly integration won't work on Mac?
 
Hi all,
 
verified that latest weekly integration from
07/05 launched okay on my Mac and I can selected items in the menu. Only
advice I can give at this point is the usual, check that you launch the
"STEM.app/Contents/MacOS/STEM" file directly, and that OS X security
setting are configured to allow launching it.
 
Regards,
/ Stefa
 
Stefan Edlund
Research Software Engineer - Industrial and Applied Genomics
IBM Research - Almaden
(408) 927-1766 sedlund@xxxxxxxxxx
 
 
----- Original message -----
From: James Kaufman/Almaden/IBM
To: Emily Nixon <emily.nixon@xxxxxxxxxxxxx>
Cc: Ahmad Swaid <Ahmad.Swaid@xxxxxxxxxxx>, Douglas Judy <judy.douglas07@xxxxxxxxx>,
Stefan Edlund <sedlund@xxxxxxxxxx>
Subject: Re: Reason why weekly integration won't work on Mac?
Date: Wed, Jul 11, 2018 12:32 PM
 
Thank you Emily. Let's try to skype each other at 9am PT

Also, it's quite likely the new STEM e4 build will fix any problems re:
Apples application security settings. If you have time you might download
the STEM e4 branch (not the master branch) from git and build it in the
development environment. It might run great for you on your machine and
you would be helping us with testing. There's an issue around icons but
it runs fine....

Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)



Emily Nixon ---07/10/2018
10:16:54 AM---Hi James, Thank you for your sympathy, it’s much appreciated.

From: Emily Nixon <emily.nixon@xxxxxxxxxxxxx>
To: James Kaufman <jhkauf@xxxxxxxxxx>
Cc: Ahmad Swaid <Ahmad.Swaid@xxxxxxxxxxx>,
Douglas Judy <judy.douglas07@xxxxxxxxx>, Stefan Edlund <sedlund@xxxxxxxxxx>
Date: 07/10/2018 10:16 AM
Subject: Re: Reason why weekly integration
won't work on Mac?

---

Hi James,

Thank you for your sympathy, it’s much appreciated. 

Due to the time difference, I assume only the morning for you would work.
Anytime between 8-10.30am Pacific time (your time) would work for me. 

Best wishes,
Emily 

On 10 Jul 2018, at 17:35, James Kaufman <jhkauf@xxxxxxxxxx>
wrote: 
Hi Emily,
Please accept my sympathy.
Are you on skype? Maybe we can do a screen share on Friday of this week.
What times work for you?

Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:        Emily
Nixon <emily.nixon@xxxxxxxxxxxxx>
To:        James Kaufman
<jhkauf@xxxxxxxxxx>,
Stefan Edlund <sedlund@xxxxxxxxxx>
Cc:        Douglas
Judy <judy.douglas07@xxxxxxxxx>,
Ahmad Swaid <Ahmad.Swaid@xxxxxxxxxxx>
Date:        07/10/2018
09:23 AM
Subject:        Re:
Reason why weekly integration won't work on Mac?

---

Hi all,

Unfortunately, I won't be able to participate in the STEM call this week
as I am at a funeral on Thursday. 

If Stefan isn't sure what the problem is from my stack trace, then I am
available for a web call on Wednesday or Friday. I know you are both are
away so it may not be possible to do this. 

I will try to update you Judy before Thursday if we have made any progress,
otherwise my update will be as you wrote in the agenda:

Emily: Working with Jamie on problem with weekly integration build on a
Mac; Stefan will take a look; 

As for the other issue you mentioned in the agenda under my name:

"earlier issues involved using disease initializer with stochastic
solver"

I haven't been able to look at since, as I am still needing to get STEM
working on my Mac. However, I will take a further look at this once STEM
is working and I am able to run my model a few more times. If it is still
a problem, then I will send a practice project to Jamie/Stefan as previously
suggested. 

Best wishes,

Emily 
  
Emily Nixon
PhD Student

Demonstrator 


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389

---

From: James Kaufman <jhkauf@xxxxxxxxxx>
Sent: 06 July 2018 17:23:10
To: Emily Nixon; Stefan Edlund
Cc: Douglas Judy; Ahmad Swaid
Subject: Re: Reason why weekly integration won't work on Mac?

Thanks Emily,
Hi Stefan, when you get back could you please take a look at the stack
trace attached below?  Emily is having trouble launching the integration
build on her mac (it works for me....)

We have a holiday this week and Stefan is traveling. We can try a web call
too....

Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:        Emily
Nixon <emily.nixon@xxxxxxxxxxxxx>
To:        James Kaufman
<jhkauf@xxxxxxxxxx>
Cc:        Emily Nixon
<emily.nixon@xxxxxxxxxxxxx>,
Stefan Edlund <sedlund@xxxxxxxxxx>,
Douglas Judy <judy.douglas07@xxxxxxxxx>
Date:        07/06/2018
02:17 AM
Subject:        Re:
Reason why weekly integration won't work on Mac?

---

Hi Jamie,

I have dowloaded STEM-3.0.0.I20180628165230-macosx.cocoa.x86_64.zip
directly from Eclipse. 

I also checked that my security settings were in line with your recommendation.
I even went further and set it to open Apps from “Anywhere” but this
still didn’t work.

I managed to get a stack trace/error log from the terminal window this
time which I have attached to see if that gives any clues.

If not, then a web conference call sounds good.

Best regards,

Emily


On 5 Jul 2018, at 18:16, James Kaufman <jhkauf@xxxxxxxxxx>
wrote:

Hi Emily,
I just downloaded the latest integration build and I was able to run it
fine on my mac. So I don't think we have a build problem.

Please download the integration build DIRECTLY from Eclipse - don't
use the "Update" button in an existing STEM installation.
The file download should be called
STEM-3.0.0.I20180628165230-macosx.cocoa.x86_64.zip
I you need to migrate workspace projects just rename the old install folder
and later you can copy projects to the new workspace (after a successful
first launch).


I'm wondering if there might be a security setting issue on your mac.

Please Open System Preferences and go to Security & Privacy, and make
sure the General tab is selected. (You'll see that this is the same page
where you tell macOS to allow apps from identified developers as well as
from the App Store.)

Click on the lock on the lower left corner and you will be asked to enter
your password to unlock the settings page.
Then select "Allow Apps" from "App Store and Identified
Developers"
You may still be told that STEM is from and Unidentified developer and
have to approve it's use on launch but this may help.

If this does not work maybe we can do a web conference call next week.
Let's keep track of both the issue and fix so we can update the wiki for
others once we understand the problem.

Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:        Emily
Nixon <emily.nixon@xxxxxxxxxxxxx>
To:        James Kaufman
<jhkauf@xxxxxxxxxx>
Date:        07/04/2018
06:39 AM
Subject:        Re:
Reason why weekly integration won't work on Mac?

---

Hi Jamie,

Please find a word document attached which answers your questions below.

I’ve tried downloading the release version which works. However, once
I've set it to install updates for the integration (so that I can have
the new stochastic solver), it then no longer works and has the same problem
as if I downloaded the weekly integration version directly (I can't click
on anything, including "file", "edit" etc.). So perhaps
it is a problem with the newest integration?

If my word document doesn't help to solve the problem, then maybe you could
send me an older weekly integration that still has the random seed option
for the stochastic solver?


Thanks so much for all of your help.

Best wishes,

Emily

Emily Nixon
PhD Student

Demonstrator


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389

---

From: James Kaufman <jhkauf@xxxxxxxxxx>
Sent: 03 July 2018 21:37:25
To: Emily Nixon
Cc: Swaid Ahmad; Judy Douglas; Stefan Edlund
Subject: Re: Reason why weekly integration won't work on Mac?

Hi Emily,
That is a bit odd. In method 2, in the console window, do you see a stack
trace or error?

Can you try the following as a test?

Method 1
After you download STEM, extract the archive and  move the STEM folder
to Applications
Navigate to Application and, using the mac FINDER,  click once to
select the file STEM.app
Then RIGHT click (two finger click) and select "Show Package Contents"
A new window will appear
open the folder labeled "Contents/MacOS"
you should see an file called STEM with the stem icon

Do a double click (one finger) on that file and select OPEN

You should get a window indicating it is a new application downloaded from
the internet.

Also, what version of Java do you have installed? Please open a console
and type >Java -version

    The first time you run STEM the workspace folder is created.
    could you please navigate to the STEM folder (where STEM.app
is installed) and see do you see a folder "workspace"?


Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email:
jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:        Emily
Nixon <emily.nixon@xxxxxxxxxxxxx>
To:        James Kaufman
<jhkauf@xxxxxxxxxx>
Cc:        Stefan
Edlund <sedlund@xxxxxxxxxx>,
Swaid Ahmad <Ahmad.Swaid@xxxxxxxxxxx>,
Judy Douglas <judy.douglas07@xxxxxxxxx>
Date:        07/03/2018
10:04 AM
Subject:        Re:
Reason why weekly integration won't work on Mac?

---

Hi Jamie,

I managed to open the STEM GUI using the second method, but it doesn’t
let me click on anything in the GUI (even close, minimise) once it’s open.

Best regards,
Emily



On 3 Jul 2018, at 17:11, James Kaufman <jhkauf@xxxxxxxxxx>
wrote:

Hi Emily,
The launch problem on Mac will get fixed when we are done with the e4 build,
but there is a workaround.

Method 1
After you download STEM, extract the archive and  move the STEM folder
to Applications
Navigate to Application and, using the mac FINDER,  click once to
select the file STEM.app
Then RIGHT click (two finger click) and select "Show Package Contents"
A new window will appear
open the folder labeled "Contents/MacOS"
you should see an file called STEM with the stem icon

Do a two finger click on that file and select OPEN



Method 2 (from a console)
Extract STEM as above
Open a console window
navigate to /Applications/stem_Integration8_18_16/STEM.app/Contents/MacOS
using
cd /Applications/stem_Integration8_18_16/STEM.app/Contents/MacOS
type
./STEM

Both methods should work
Please let me know if that works or if you have problems.






Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:        Emily
Nixon <emily.nixon@xxxxxxxxxxxxx>
To:        James Kaufman
<jhkauf@xxxxxxxxxx>,
'Stefan Edlund' <sedlund@xxxxxxxxxx>
Date:        07/03/2018
07:44 AM
Subject:        Reason
why weekly integration won't work on Mac?

---

Hi Jamie and Stefan,

I have now got a Macbook pro which should help with using STEM.

However, I can only seem to get the Release version to work and not the
Weekly Integration version. I would like to use the Weekly Integration
version as it has the new randomise seed option for the stochastic solver.
Do you know of any reason why it might not be working for me?

I follow the installation instructions and manage to open STEM, but then
I can't seem to interact with it. It won't let me click on anything (e.g.
to close the welcome screen, minimise or make it full screen). This doesn't
happen with the release version when I install it in the same way.

If you have any idea what might be going on, then let me know!

Hope you're both doing well.

Best wishes,

Emily 
Emily Nixon
PhD Student

Demonstrator


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389

[attachment "weeklyIntegrationDownloadIssues.docx" deleted by
James Kaufman/Almaden/IBM] 


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