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I am doing my master's and I am considering doing my PhD at a different institution. I asked my advisor for reference and he was fine with it. My co-advisor insisted on me staying. I tried to talk him multiple times to be able to leave on good terms before I started applying and he was very reluctant to me leaving. My discussions with him were not productive and every time he starts suggesting projects for me and tries to convince me to stay. Discussion gets heated when I say I want to leave my options open and ends that way. I have to say that he is a very good advisor, but that reason is not enough for me to stay.

I decided to apply without letting him know and I did. My advisor is now asking me to let my co-advisor know that I am applying, and that I owe him that. I am sure he will be very angry and another heated argument will start again. What to do in a such a situation?

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    Have you got an offer from another institution to do the PHD there? Since, you are now at the stage of getting reference letters probably not. So, you are actually not leaving but THINKING OF leaving. This difference is crucial. So, ask for the reference, say that you consider of leaving and you need to explore all possibilities. This will make getting the reference letter easier and you will still have a backup plan if your original plan (of leaving) fails. – Alexandros Nov 17 '14 at 10:47
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    Something is missing from this picture. What are your goals and how do you feel they are better served at a different institution? Without the basic facts of your decision, the question basically boils down to a difference of opinion (where of course, this being your life, your own opinion should prevail; but it's hard for us to assess why your co-advisor insists on a different outcome). – tripleee Nov 17 '14 at 11:48
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    The institution is still new, and while the level of research in my department is excellent, other departments have a bad reputation. Up to now, there are no PhD graduates from my current institution which makes getting a job difficult afterwards and I believe I can go to an institution with a better ranking. – user18244 Nov 17 '14 at 12:41
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    @tripleee: that's irrelevant to the question. The point here is that the co-advisor is being extremely unprofessional. – Martin Argerami Nov 17 '14 at 12:42
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    I have to say that he is a very good advisor — I strongly disagree. – JeffE Nov 18 '14 at 4:14
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Tell your co-advisor. If he doesn't react well, take your advisor with you and have a second meeting. Maybe they can work it out colleague to colleague rather than professor to student. Withholding a good letter of recommendation because you want a promising student to stay and work with you is extremely selfish and borderline misconduct.

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You will finish your Master's before you leave, right? In that case, there shouldn't be any obligation for you to stay. Just tell your co-advisor that you're applying to a different institution.

It's your life and your decision. There's nothing to argue about. Honestly, if you tell him in person (or it comes up in a later meeting) and it starts to turn into an argument, just tell him you don't want to argue about it. If he continues, don't argue. Just get up and leave.

A calm discussion is fine if he wants to convince you to stay - let him present his counter-offer calmly if he wants to. My advice for dealing with anger is no different than dealing with arguments with anyone else, either personal or professional - if their anger is controlling the situation, just leave.

It's a shame that an otherwise-good advisor is so "clingy", but don't let that get in the way of what you want to do. If either advisor has an iota of professionalism, they won't let their personal wishes affect your reference letters. Perhaps it's for the better - having a volatile and possessive supervisor overseeing your PhD could lead to more problems later.

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